expression.dst

[templateStart]
name=PageProfileSetParamQuery
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
>templateTextStart<
      <sqlQuery name="${datasetName}PageProfiles" includeProjects="${includeProjectsExcludeEuPathDB}">
             <column name="display"/>
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
select distinct s.node_set_id as internal
     , s.name as term
     , REGEXP_REPLACE (s.name, '\[(.)+\]', '')  AS display
     , d.name
from study.nodeset s
   , apidbtuning.NodeSetOutputNode sl
   , RESULTS.NAFEATUREDIFFRESULT dr
   , SRES.EXTERNALDATABASERELEASE r
   , sres.externaldatabase d
where
s.EXTERNAL_DATABASE_RELEASE_ID = r.EXTERNAL_DATABASE_RELEASE_ID
and r.EXTERNAL_DATABASE_ID = d.EXTERNAL_DATABASE_ID
and s.node_set_id = sl.node_set_id
and sl.PROTOCOL_APP_NODE_ID = dr.PROTOCOL_APP_NODE_ID
and d.name = '${datasetName}'
ORDER BY s.name desc
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}PageProfiles" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB"> 
            <wsColumn name="display" width="300"/>
            <wsColumn name="internal" width="300"/>
            <wsColumn name="term" width="300"/>
        </processQuery>
>templateTextEnd<


[templateStart]
name=expressionProfileSetParamQuery
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetNamePattern
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=decodeProfileSet
prop=excludedProfileSetsList
prop=dataType
>templateTextStart<
      <sqlQuery name="${datasetName}${dataType}Profiles" includeProjects="${includeProjectsExcludeEuPathDB}">
             <column name="display"/>
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
with p as (select profile_study_id , profile_set_name
    from apidbtuning.profiletype pt, 
         (select distinct sl.node_set_id as study_id
          from apidbtuning.NodeSetOutputNode sl, apidbtuning.PanResults panr
          where sl.protocol_app_node_id = panr.pan_id
          and panr.result_table = 'Results::NAFeatureExpression') dr
    where (dataset_name = '${datasetName}' OR dataset_name like '${datasetNamePattern}')
    and pt.profile_set_name not in ( ${excludedProfileSetsList})
    and pt.profile_type = 'values'
    and pt.profile_study_id = dr.study_id
    ),
  ct as (select count(*) as total from p) 
select  profile_study_id as internal, profile_set_name as term,
        case when (my_ct.total =1) 
             then CASE WHEN profile_set_name ='' THEN '' ELSE  ${decodeProfileSet}  '${datasetDisplayName}' END
             else profile_set_name end as display
from ct my_ct, p
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}${dataType}Profiles" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB"> 
            <wsColumn name="display" width="200"/>
            <wsColumn name="internal" width="200"/>
            <wsColumn name="term" width="200"/>
        </processQuery>
>templateTextEnd<


[templateStart]
name=expressionPctProfileSetParamQuery
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetNamePattern
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=decodeProfileSet
prop=excludedProfileSetsList
prop=dataType
>templateTextStart<
      <sqlQuery name="${datasetName}${dataType}PctProfiles" includeProjects="${includeProjectsExcludeEuPathDB}">
             <column name="display"/>
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
SELECT DISTINCT profile_study_id AS internal, profile_set_name AS term,
                 CASE WHEN ps.name = '' THEN '' ELSE ${decodeProfileSet}  '${datasetDisplayName}' END as display
FROM apidbtuning.profileType
WHERE dataset_name = '${datasetName}'
AND profile_set_name not in ( ${excludedProfileSetsList})
AND profile_type like '%percentile%'
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}${dataType}PctProfiles" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB"> 
            <wsColumn name="display" width="200"/>
            <wsColumn name="internal" width="200"/>
            <wsColumn name="term" width="200"/>
        </processQuery>
>templateTextEnd<


[templateStart]
name=expressionFoldChangeQuestion
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=isLogged
prop=dynColSuffix
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
prop=defaultFoldDifference
prop=datasetFloor
prop=floorText
>templateTextStart<
    <question name="GenesBy${dataType}${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (fold change)"
         shortDisplayName="${datasetShortDisplayName} (fc)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByGenericFoldChange"
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
        <paramRef ref="geneParams.profileset_generic" groupRef="paramGroups.dynamicParams" queryRef="GeneVQ.${datasetName}${dataType}Profiles"/>
        <paramRef groupRef="paramGroups.dynamicParams" ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 
        <paramRef groupRef="paramGroups.dynamicParams" ref="geneParams.fold_change" default="${defaultFoldDifference}"/>
<paramRef ref="geneParams.hard_floor" groupRef="paramGroups.dynamicParams" default="${datasetFloor}"/>
	<sqlParamValue name="isLogged">${isLogged}</sqlParamValue>
	<attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
	   summary="organism,gene_product,fold_change_chosen,chose_group_two,chose_group_one,exprGraphAttr${datasetName}_expr_graph"
	   sorting="fold_change_avg desc" /> 
        
        <attributesList includeProjects="EuPathDB"
         summary="organism,gene_product,fold_change_chosen_display,chose_group_two,chose_group_one"
         sorting="fold_change_chosen_display desc"  /> 

         <summary>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.
           ]]>
         </summary>

         <description>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.  First choose an experiment as the available samples may change.  If only one "Experiment" is shown, this field will be selected for you.
<br/><br/>
After selecting samples you have the option to take the average, minimum, or maximum expression value within each group.  (If choosing only one sample from a group, the selected 'operation' will not affect your results).  Time series experiments will offer an extra parameter called "Global min/max" which allows you to filter your results further.  Finally, you can choose the directionality and the magnitude of the difference.  For example, selecting up-regulated with a fold difference of 2 will only show results where the comparator is twice that of the reference.
<br/><br/>
${floorText}
<br/><br/>
${optionalQuestionDescription}
          ]]>
         </description>



        <dynamicAttributes>
           <columnAttribute name="fold_change_avg" displayName="Fold Difference (Avg)" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="fold_change_chosen" displayName="Fold Difference" align="center" help="${floorText}">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="fold_change_chosen_display" displayName="Fold Difference Display" align="center" inReportMaker="false" help="* indicates that the chosen reference has been set to the floor in order to compute the fold change"/>
           <columnAttribute name="avg_group_one" displayName="Avg Comp${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="avg_group_two" displayName="Avg Ref${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="min_group_one" displayName="Min Comp${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="min_group_two" displayName="Min Ref${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="max_group_one" displayName="Max Comp${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="max_group_two" displayName="Max Ref${dynColSuffix}" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="chose_group_one" displayName="Chosen Comp${dynColSuffix}" align="center" help="This number represents the expression value calculated for the 'Comparison Samples' and 'Operation Applied to Comparison Samples' that you chose when setting up the fold change search.">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="chose_group_two" displayName="Chosen Ref${dynColSuffix}" align="center" help="This number represents the expression value calculated for the 'Reference Samples' and 'Operation Applied to Reference Samples' that you chose when setting up the fold change search.">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
        </dynamicAttributes>



       <propertyList name="displayCategory">
           <value>fold_change</value>
       </propertyList>

    </question>
>templateTextEnd<

[templateStart]
name=expressionPercentileQuestion
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
>templateTextStart<
    <question name="GenesBy${dataType}${datasetName}Percentile" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (percentile)"
         shortDisplayName="${datasetShortDisplayName} (%ile)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByGenericPercentile" 
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">

        <paramRef ref="geneParams.profileset_generic" queryRef="GeneVQ.${datasetName}${dataType}Profiles"/>
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 

        <attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
              summary="gene_product,min_percentile_chosen,max_percentile_chosen,pctGraphAttr${datasetName}_pct_graph"
              sorting="max_percentile_chosen desc"
        /> 
        <attributesList includeProjects="EuPathDB"
              summary="gene_product,min_percentile_chosen,max_percentile_chosen"
              sorting="max_percentile_chosen desc"
        /> 

        <summary>
           <![CDATA[
Find genes which are expressed in a ${dataType} experiment.
         ]]>
        </summary>

        <description>
           <![CDATA[
Find genes which are expressed in a ${dataType} experiment.  For each Experiment and Sample, genes were ranked by expression level.  This search enables you to find genes w/in a specified range of values.  This search does allow you to search for genes with low levels of expression, however, care should be taken when drawing conclusions because there are many factors which may contribute to a negative result.
<br /><br/>
${optionalQuestionDescription}

      ]]>
        </description>

       <dynamicAttributes>
	     <columnAttribute name="min_percentile_chosen" displayName="Min %ile (Within Chosen Samples)" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	     </columnAttribute>
	     <columnAttribute name="max_percentile_chosen" displayName="Max %ile (Within Chosen Samples)" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	     </columnAttribute>
	</dynamicAttributes>

       <propertyList name="displayCategory">
           <value>percentile</value>
       </propertyList>


    </question>
>templateTextEnd<


[templateStart]
name=expressionFoldChangeWithConfidenceQuestion
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=isLogged
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
>templateTextStart<
    <question name="GenesBy${dataType}${datasetName}Confidence" includeProjects="${includeProjects}"  newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (fold change w/ confidence)"
         shortDisplayName="${datasetShortDisplayName} (fc w/ conf)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByGenericFoldChangeWithConfidence"
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
        <!-- params we are overriding -->


        <paramRef ref="geneParams.profileset_generic" queryRef="GeneVQ.${datasetName}${dataType}Profiles" />
        <paramRef ref="geneParams.samples_fc_ref_generic" visible="true" multiPick="false" />
        <paramRef ref="geneParams.samples_fc_comp_generic" multiPick="false"/> 
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 
	<sqlParamValue name="isLogged">${isLogged}</sqlParamValue>

        <attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
         summary="organism,gene_product,fold_change,confidence,exprGraphAttr${datasetName}_expr_graph"
         sorting="fold_change_avg asc"         
         /> 

         <attributesList includeProjects="EuPathDB"
          summary="organism,gene_product,fold_change,confidence"
          sorting="fold_change_avg asc"         
         /> 


         <summary>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.
           ]]>
         </summary>

         <description>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment using <a href="http://www.cbil.upenn.edu/PaGE/">PaGE</a>.  Each sample is available to compare to every other sample.  First choose an experiment as the available samples may change.  If only one "Experiment" is shown, this field will be selected for you.
<br/><br/>
Choose reference and comparator samples then you can choose the directionality and the magnitude of the difference.  For example, selecting up-regulated with a fold difference of 2 will only show results where the comparator is twice that of the reference.  This search also requires that you choose a confidence (0-1) cut off to filter results.  Results w/ a high confidence are less likely to be false positives relative to those close to zero.
<br /><br/>
${optionalQuestionDescription}

          ]]>
         </description>
       
         <dynamicAttributes>
           <columnAttribute name="fold_change" displayName="Fold Difference" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
  	   </columnAttribute>
           <columnAttribute name="confidence" displayName="Confidence" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	   </columnAttribute>
         </dynamicAttributes>


       <propertyList name="displayCategory">
           <value>fold_change_with_confidence</value>
       </propertyList>


     </question>
>templateTextEnd<


[templateStart]
name=expressionGraphAttributesPathwayRecord
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/pathwayRecord.xml
prop=presenterId
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=graphModule
prop=graphTextAttrName
prop=datasetDisplayName
prop=shortAttribution
prop=organismAbbrevDisplay
>templateTextStart<
	   <textAttribute name="${graphTextAttrName}"
			  displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${shortAttribution}"
			  truncateTo="100000" sortable="false"
			  includeProjects="${includeProjectsExcludeEuPathDB}">
              <text>
                <![CDATA[
                /cgi-bin/dataPlotter.pl?idType=ec&fmt=png&type=${graphModule}&project_id=${projectName}&datasetId=${presenterId}&default=1&template=1&id=
                ]]>
              </text>
	   </textAttribute>
>templateTextEnd<


[templateStart]
name=expressionGraphAttributesExpression
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
prop=datasetName
prop=presenterId
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=graphModule
prop=exprGraphVisiblePart
prop=graphTextAttrName
>templateTextStart<
	   <textAttribute name="${graphTextAttrName}"
			  displayName="${datasetShortDisplayName} - Expr Graph"
			  inReportMaker="false" truncateTo="100000" sortable="false"
			  includeProjects="${includeProjectsExcludeEuPathDB}">
              <text>
                <![CDATA[
                                <a href="@WEBAPP_BASE_URL@/record/gene/$$gene_source_id$$#category:transcriptomics">
                <img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&template=1&fmt=png&id=$$primary_key$$&datasetId=${presenterId}&vp=${exprGraphVisiblePart}&vpAreFuzzy=1&thumb=1"/>
				</a>
                ]]>
              </text>
	   </textAttribute>
>templateTextEnd<

[templateStart]
name=expressionGraphAttributesPercentile
anchorFile=ApiCommonModel/Model/lib/wdk/model/records/transcriptRecord.xml
prop=datasetName
prop=presenterId
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=dataType
prop=graphModule
prop=graphTextAttrName
>templateTextStart<
	   <textAttribute name="pctGraphAttr${datasetName}_pct_graph"
			  displayName="${datasetShortDisplayName} - %ile Graph"
			  inReportMaker="false" truncateTo="100000" sortable="false"
			  includeProjects="${includeProjectsExcludeEuPathDB}">
              <text>
                <![CDATA[
                                <a href="@WEBAPP_BASE_URL@/record/gene/$$gene_source_id$$#category:transcriptomics">
                <img src="/cgi-bin/dataPlotter.pl?type=${graphModule}&project_id=${projectName}&template=1&fmt=png&id=$$primary_key$$&datasetId=${presenterId}&vp=percentile&vpAreFuzzy=1&thumb=1"/>
                </a>
				]]>
              </text>
	   </textAttribute>
>templateTextEnd<


[templateStart]
name=expressionSamplesParamQueryDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetNamePattern
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=excludedProfileSetsList
prop=dataType
>templateTextStart<
      <sqlQuery name="${datasetName}${dataType}Samples" includeProjects="${includeProjectsExcludeEuPathDB}">
             <paramRef ref="geneParams.profileset_generic"/>
             <column name="display"/>
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
	      SELECT  ps.protocol_app_node_id as internal, ps.protocol_app_node_name as display, 
	         ps.protocol_app_node_name as term
	      FROM apidbtuning.ProfileSamples ps
	      WHERE ps.study_id = $$profileset_generic$$
	      AND profile_type='values'
	      ORDER BY ps.node_order_num
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}${dataType}Samples" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB"> 
             <paramRef ref="geneParams.profileset_generic"/> 
            <wsColumn name="display" width="200"/>
            <wsColumn name="internal" width="200"/>
            <wsColumn name="term" width="200"/>
        </processQuery>
>templateTextEnd<

[templateStart]
name=expressionSamplesParamQueryDirectFDR
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetNamePattern
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=excludedProfileSetsList
prop=dataType
>templateTextStart<
      <sqlQuery name="${datasetName}${dataType}DirectFDRSamples" includeProjects="${includeProjectsExcludeEuPathDB}">
             <paramRef ref="geneParams.profileset_generic"/>
             <column name="display"/>
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
         SELECT pen.name as term,
                pen.profile_element_name_id as internal, 
                pen.name as display
          FROM apidb.profileelementname pen,apidb.profileset ps
          WHERE pen.profile_set_id =  ps.profile_set_id
          and pen.profile_set_id = $$profileset_generic$$
          and lower(ps.name) not like '%percentile%'
          and ps.name not like 'standard error%'
          and ps.name not in ( ${excludedProfileSetsList})
          order by pen.element_order
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}${dataType}DirectFDRSamples" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB">
            <paramRef ref="geneParams.profileset_generic"/> 
            <wsColumn name="display" width="200"/>
            <wsColumn name="internal" width="200"/>
            <wsColumn name="term" width="200"/>
        </processQuery>
>templateTextEnd<




[templateStart]
name=expressionPctSamplesParamQueryDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/params/geneParams.xml
prop=datasetName
prop=datasetDisplayName 
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=channelOnePctSampleDecode
prop=channelTwoPctSampleDecode
prop=percentileProfileSetPattern
prop=dataType
>templateTextStart<
      <sqlQuery name="${datasetName}${dataType}PctSamples" includeProjects="${includeProjectsExcludeEuPathDB}">
             <paramRef ref="geneParams.profileset_generic"/>    
             <paramRef ref="geneParams.channel"/>    
             <column name="internal"/>
             <column name="term"/>
          <sql>
           <![CDATA[
	      SELECT  protocol_app_node_id as internal,
	      CASE WHEN  ('$$channel$$' ='channel1') THEN
                CASE WHEN protocol_app_node_name = '' THEN '' ELSE ${channelOnePctSampleDecode}
                       protocol_app_node_name END
		ELSE CASE WHEN protocol_app_node_name = '' THEN '' ELSE ${channelTwoPctSampleDecode}
                       protocol_app_node_name END
		    END as term
	      FROM apidbtuning.ProfileSamples ps
	      WHERE ps.study_id = $$profileset_generic$$	
	      AND profile_type like '%' || '$$channel$$' || '%'
	      ORDER BY ps.node_order_num
            ]]>
          </sql>
        </sqlQuery>
        <processQuery name="${datasetName}${dataType}PctSamples" processName="org.apidb.apicomplexa.wsfplugin.apifed.ApiFedPlugin" includeProjects="EuPathDB"> 
            <paramRef ref="geneParams.profileset_generic"/>    
             <paramRef ref="geneParams.channel"/>    
            <wsColumn name="internal" width="200"/>
            <wsColumn name="term" width="200"/>
        </processQuery>
>templateTextEnd<

[templateStart]
name=expressionFoldChangeQuestionDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=isLogged
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
prop=defaultFoldDifference
>templateTextStart<
    <question name="GenesBy${dataType}Direct${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (direct comparison)"
         shortDisplayName="${datasetShortDisplayName} (dc)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByDirectComparisonGeneric" 
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
        <paramRef ref="geneParams.profileset_generic" groupRef="paramGroups.dynamicParams" queryRef="GeneVQ.${datasetName}${dataType}Profiles"/>
        <paramRef ref="geneParams.samples_fc_ref_generic" queryRef="GeneVQ.${datasetName}${dataType}Samples" prompt="Comparison" multiPick="false"/>
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 
        <paramRef ref="geneParams.fold_difference" default="${defaultFoldDifference}"/>
	<sqlParamValue name="isLogged">${isLogged}</sqlParamValue>

	<attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
            summary="organism,gene_product,fold_difference,exprGraphAttr${datasetName}_expr_graph"
            sorting="fold_difference desc"/>
        <attributesList includeProjects="EuPathDB"
           summary="organism,gene_product,fold_difference"
           sorting="fold_difference desc"  /> 


         <summary>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.
           ]]>
         </summary>

         <description>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.  First choose a Sample Comparison and a Direction.  Sample Comparisons are listed as "A vs. B".  Up regulated genes will be genes with higher expression in A as compared to B.  You can also filter your results based on the magnitued of the difference.  For example, selecting up-regulated with a fold difference of 2 will only show results where the comparator (A) is twice that of the reference (B).
<br /><br/>
${optionalQuestionDescription}

          ]]>
         </description>

        <dynamicAttributes>
           <columnAttribute name="fold_difference" displayName="Fold Difference" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	   </columnAttribute>
        </dynamicAttributes>

       <propertyList name="displayCategory">
           <value>fold_change</value>
       </propertyList>


    </question>
>templateTextEnd<



[templateStart]
name=expressionFoldChangeWithConfidenceQuestionDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
>templateTextStart<
    <question name="GenesBy${dataType}DirectWithConfidence${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (direct comparison)"
         shortDisplayName="${datasetShortDisplayName} (dc)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByDirectComparisonGenericPage" 
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">

        <paramRef ref="geneParams.profileset_generic"  queryRef="GeneVQ.${datasetName}PageProfiles" visible="false"/>
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 

	<attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
            summary="organism,gene_product,fold_change,exprGraphAttr${datasetName}_expr_graph"
            sorting="fold_change desc"/>
        <attributesList includeProjects="EuPathDB"
           summary="organism,gene_product,fold_change"
           sorting="fold_change desc"  /> 


         <summary>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.
           ]]>
         </summary>

         <description>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment using <a href="http://www.cbil.upenn.edu/PaGE/">PaGE</a>.  First choose a Sample Comparison and a Direction.  Sample Comparisons are listed as "A vs. B".  Up regulated genes will be genes with higher expression in A as compared to B.  You can also filter your results based on the magnitued of the difference.  For example, selecting up-regulated with a fold difference of 2 will only show results where the comparator is twice that of the reference.  This query also requires that you choose a confidence (0-1) cut off to filter results.  Results w/ a high confidence are less likely to be false positives relative to those close to zero.
<br /><br/>
${optionalQuestionDescription}

          ]]>
         </description>


        <dynamicAttributes>
           <columnAttribute name="fold_change" displayName="Fold Difference" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="confidence" displayName="Confidence" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>

        </dynamicAttributes>

       <propertyList name="displayCategory">
           <value>fold_change_with_confidence</value>
       </propertyList>


    </question>
>templateTextEnd<

[templateStart]
name=expressionFoldChangeWithFDRQuestionDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
prop=defaultFoldDifference
>templateTextStart<
    <question name="GenesBy${dataType}DirectWithFDR${datasetName}" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (direct comparison w/ false discovery rate)"
         shortDisplayName="${datasetShortDisplayName} (dc w/ fdr)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByDirectComparisonGenericFDR" 
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
         
        <paramRef ref="geneParams.profileset_generic" queryRef="GeneVQ.${datasetName}${dataType}Profiles"/>
        <paramRef ref="geneParams.samples_direct_comp_fdr_generic" queryRef="GeneVQ.${datasetName}${dataType}DirectFDRSamples" />
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 
        <paramRef ref="geneParams.fold_difference" default="${defaultFoldDifference}"/>
	<attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
            summary="organism,gene_product,fold_change,false_discovery_rate,exprGraphAttr${datasetName}_expr_graph"
            sorting="fold_change desc"/>
        <attributesList includeProjects="EuPathDB"
           summary="organism,gene_product,fold_change"
           sorting="fold_change desc"  /> 


         <summary>
            <![CDATA[
Find genes which are differentially expressed in a ${dataType} experiment.
           ]]>
         </summary>

         <description>
            <![CDATA[
Find genes that are differentially expressed between the samples of a proteomics experiment.</br>
Sample comparisons are listed as "A vs. B" so up-regulated genes have higher expression in Sample A than in B.</br> 
The fold difference parameter filters results based on the magnitude of difference in expression between samples A and B. For example, selecting up-regulated with a fold difference >= 2 will return genes with expression in Sample A at least twice that in sample B.</br>
The false discovery rate parameter defines a statistical confidence for genes returned by the search. Results with a lower false discovery rate are more likely to be true positives.
<br /><br/>
${optionalQuestionDescription}

          ]]>
         </description>


        <dynamicAttributes>
           <columnAttribute name="fold_change" displayName="Fold Difference" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
           <columnAttribute name="false_discovery_rate" displayName="false_discovery_rate" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
        </dynamicAttributes>

       <propertyList name="displayCategory">
           <value>fold_change_with_confidence</value>
       </propertyList>


    </question>
>templateTextEnd<

[templateStart]
name=expressionPercentileQuestionDirect
anchorFile=ApiCommonModel/Model/lib/wdk/model/questions/geneQuestions.xml
prop=datasetName
prop=datasetDisplayName 
prop=datasetShortDisplayName
prop=includeProjectsExcludeEuPathDB
prop=projectName
prop=buildNumberIntroduced
prop=hasTimeSeries
prop=isEuPathDBSite
prop=includeProjects
prop=optionalQuestionDescription
prop=organismAbbrevDisplay
prop=dataType
prop=defaultProteinCodingOnly
prop=proteinCodingParamVisible
>templateTextStart<
    <question name="GenesBy${dataType}Direct${datasetName}Percentile" includeProjects="${includeProjects}" newBuild="${buildNumberIntroduced}"
         displayName="${organismAbbrevDisplay} ${datasetDisplayName} ${dataType} (percentile)"
         shortDisplayName="${datasetShortDisplayName} (%ile)"
         searchCategory="Transcript Expression"
         queryRef="GeneId.GenesByGenericPercentile" 
         recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">

        <paramRef ref="geneParams.profileset_generic" queryRef="GeneVQ.${datasetName}${dataType}Profiles" visible="false"/>
        <paramRef ref="geneParams.samples_percentile_generic" queryRef="GeneVQ.${datasetName}${dataType}PctSamples"/>
        <paramRef ref="geneParams.protein_coding_only" default="${defaultProteinCodingOnly}" visible="${proteinCodingParamVisible}"/> 
        <paramRef ref="geneParams.channel" visible="true"/>
        <attributesList includeProjects="${includeProjectsExcludeEuPathDB}"
              summary="gene_product,min_percentile_chosen,max_percentile_chosen,pctGraphAttr${datasetName}_pct_graph"
              sorting="max_percentile_chosen desc"
        /> 
        <attributesList includeProjects="EuPathDB"
              summary="gene_product,min_percentile_chosen,max_percentile_chosen"
              sorting="max_percentile_chosen desc"
        /> 



        <summary>
           <![CDATA[
Find genes which are expressed in a ${dataType} experiment.
         ]]>
        </summary>

        <description>
           <![CDATA[
Find genes which are expressed in a ${dataType} experiment.  For each Experiment and Sample, genes were ranked by expression level.  This search enables you to find genes w/in a specified range of values.  This search does allow you to search for genes with low levels of expression, however, care should be taken when drawing conclusions because there are many factors which may contribute to a negative result.
<br /><br/>
NOTE:  For Two Channel Direct Comparison ${dataType}s the Percentiles are calculated using raw intensities.
<br /><br/>
${optionalQuestionDescription}

      ]]>
        </description>

       <dynamicAttributes>
	     <columnAttribute name="min_percentile_chosen" displayName="Min %ile (Within Chosen Samples)" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>
	     <columnAttribute name="max_percentile_chosen" displayName="Max %ile (Within Chosen Samples)" align="center">
	        <reporter name="histogram" displayName="Histogram" scopes=""                                                                     
                  implementation="org.gusdb.wdk.model.report.reporter.HistogramAttributeReporter">                                               
                  <description>Display the histogram of the values of this attribute</description>                                               
                  <property name="type">int</property>
                </reporter>
	  </columnAttribute>

	</dynamicAttributes>


       <propertyList name="displayCategory">
           <value>percentile</value>
       </propertyList>


    </question>
>templateTextEnd<