Skip to content

Commit 2928a58

Browse files
ninaxiong11ninaxiong11
authored
Merge pull request #2027 from ninaxiong11/genephylomodeler
Add test data for codeml site model
2 parents a57cfb2 + e1a38a7 commit 2928a58

16 files changed

Lines changed: 71 additions & 31 deletions

‎data/Mx_aln.phy‎

Lines changed: 14 additions & 0 deletions
Large diffs are not rendered by default.

‎data/Mx_root.tree‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
12 1
2+
((((((Chimpanzee_Mx,Human_Mx),Orangutan_Mx),Rhesus_macaque_Mx),(((Sheep_Mx,Cow_Mx),Pig_Mx),Dog_Mx)),(Mouse_Mx,Rat_Mx)),(Duck_Mx,Chicken_Mx));

‎data/Mx_unroot.tree‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
12 1
2+
((((((Chimpanzee_Mx,Human_Mx),Orangutan_Mx),Rhesus_macaque_Mx),(((Sheep_Mx,Cow_Mx),Pig_Mx),Dog_Mx)),(Mouse_Mx,Rat_Mx)),Duck_Mx,Chicken_Mx);

‎data/codeml-M0.ctl‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,19 @@
1+
seqfile = Mx_aln.phy * Path to the alignment file
2+
treefile = Mx_unroot.tree * Path to the tree file
3+
outfile = out_M0.txt * Path to the output file
4+
5+
noisy = 3 * How much rubbish on the screen
6+
verbose = 1 * More or less detailed report
7+
8+
seqtype = 1 * Data type
9+
ndata = 1 * Number of data sets or loci
10+
icode = 0 * Genetic code
11+
cleandata = 0 * Remove sites with ambiguity data?
12+
13+
model = 0 * Models for ω varying across lineages
14+
NSsites = 0 * Models for ω varying across sites
15+
CodonFreq = 7 * Codon frequencies
16+
estFreq = 0 * Use observed freqs or estimate freqs by ML
17+
clock = 0 * Clock model
18+
fix_omega = 0 * Estimate or fix omega
19+
omega = 0.5 * Initial or fixed omega

‎samplesheet/test_absrel_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
gene_name,alignment,tree,suite,tool
2-
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,absrel
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,absrel,

‎samplesheet/test_bgm_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
gene_name,alignment,tree,suite,tool
2-
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,bgm
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,bgm,

‎samplesheet/test_busted_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
gene_name,alignment,tree,suite,tool
2-
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,busted
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,busted,

‎samplesheet/test_codeml_samplesheet.csv‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
gene_name,alignment,tree,suite,tool,control_file
2+
Mx,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/Mx_aln.phy,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/Mx_unroot.tree,paml,codeml,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/codeml-sites.ctl

‎samplesheet/test_fade_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
gene_name,alignment,tree,suite,tool
2-
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.faa,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fade,

‎samplesheet/test_fel_samplesheet.csv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
1-
gene_name,alignment,tree,suite,tool
2-
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fel
1+
gene_name,alignment,tree,suite,tool,control_file
2+
KSR2,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.fna,https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/genephylomodeler/data/ksr2.tree,hyphy,fel,

0 commit comments

Comments
 (0)