From 4eef6cdbe4501f78ec92b640f1e4ab7fd524c872 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 23 Nov 2023 14:23:44 +0100
Subject: [PATCH 1/3] matchms networking: skip configfile

not necessary. also all quotes. and remove linebreaks
---
 tools/matchms/matchms_networking.xml | 32 +++++++++++-----------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
index def656099..3f36719dc 100644
--- a/tools/matchms/matchms_networking.xml
+++ b/tools/matchms/matchms_networking.xml
@@ -17,7 +17,19 @@
     </requirements>
 
     <command detect_errors="aggressive"><![CDATA[
-        sh ${matchms_networking_cli}
+        python3 '${__tool_directory__}/matchms_networking_wrapper.py'
+            --score_name '${score_layer_name}'
+            --graph_format '$graph_format'
+            --identifier '$identifier_key'
+            --top_n '$top_n'
+            --max_links '$max_links'
+            --score_cutoff '$score_cutoff'
+            --link_method '$link_method'
+            #if $keep_unconnected_nodes
+            --keep_unconnected_nodes
+            #end if
+            '$scores'
+            '$similarity_network_file'
     ]]></command>
 
     <environment_variables>
@@ -25,24 +37,6 @@
         <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
     </environment_variables>
 
-    <configfiles>
-        <configfile name="matchms_networking_cli">
-            python3 ${__tool_directory__}/matchms_networking_wrapper.py \
-            --score_name '${score_layer_name}' \
-            --graph_format '$graph_format' \
-            --identifier '$identifier_key' \
-            --top_n '$top_n' \
-            --max_links '$max_links' \
-            --score_cutoff '$score_cutoff' \
-            --link_method '$link_method' \
-            #if $keep_unconnected_nodes
-            --keep_unconnected_nodes \
-            #end if
-            '$scores' \
-            '$similarity_network_file'
-        </configfile>
-    </configfiles>
-
     <inputs>
         <param label="Similarity scores" name="scores" type="data" format="json"
             help="matchms similarity-scores file."/>

From e18ba723cf32411fb91b36ba3220fc6bef5505e5 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 23 Nov 2023 14:49:00 +0100
Subject: [PATCH 2/3] add test with wrong id key

this currently only gives a python Traceback that is hard to
read by the user. Can this be improved in the wrapper / matchms?
---
 tools/matchms/matchms_networking.xml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
index 3f36719dc..7fefa2764 100644
--- a/tools/matchms/matchms_networking.xml
+++ b/tools/matchms/matchms_networking.xml
@@ -84,6 +84,19 @@
     </outputs>
 
     <tests>
+
+        <test expect_exit_code="1" expect_failure="true">
+            <param name="scores" value="scores.json" ftype="json"/>
+            <param name="graph_format" value="cyjs"/>
+            <param name="max_links" value="5"/>
+            <param name="score_cutoff" value="0.3"/>
+            <param name="identifier_key" value="COMPOUND_NAME"/>
+            <param name="keep_unconnected_nodes" value="false"/>
+            <assert_stderr>
+                <has_text text="ValueError: None cannot be a node"/>
+            </assert_stderr>
+        </test>
+
         <test>
             <param name="scores" value="scores.json" ftype="json"/>
             <param name="graph_format" value="graphml"/>

From 07571f550d65924cca5edf5b040b7fec62f21526 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 23 Nov 2023 14:51:30 +0100
Subject: [PATCH 3/3] bump

---
 tools/matchms/matchms_networking.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/matchms/matchms_networking.xml b/tools/matchms/matchms_networking.xml
index 7fefa2764..89d763e2c 100644
--- a/tools/matchms/matchms_networking.xml
+++ b/tools/matchms/matchms_networking.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy0" profile="21.09">
+<tool id="matchms_networking" name="matchms networking" version="@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>create similarity network graph from matchms similarity scores</description>
 
     <macros>