Skip to content

Commit

Permalink
codeml: fix test parameters (#4216)
Browse files Browse the repository at this point in the history 
* codeml: fix test parameters

and make all outputs valid cheetah placeholders

* correct bump
  • Loading branch information
@bernt-matthias
bernt-matthias authored Nov 27, 2021
1 parent dc7c7e8 commit 6ecdbaa
Showing 1 changed file with 23 additions and 23 deletions.
46 changes: 23 additions & 23 deletions tools/codeml/codeml.xml
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy1" profile="18.01">
<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01">
<description>
Detects positive selection (paml package)
</description>
Expand Down Expand Up @@ -238,39 +238,39 @@ codeml '$codeml_ctl'

<outputs>
<data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" />
<data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
<data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" >
<filter>adv['seqtype']=="1"</filter>
</data>
<data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
<data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" >
<filter>adv['seqtype']=="1"</filter>
</data>
<data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
<data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" >
<filter>adv['seqtype']=="1"</filter>
</data>
<data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/>
<data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/>
<data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/>
<data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/>
<data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/>
<data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
<data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc">
<filter>adv['verbose']=="1"</filter>
</data>
</outputs>

<tests>
<test>
<test expect_num_outputs="9">
<conditional name="compat_model" >
<param name="brmodel" value="0" />
<param name="NSsites" value="0" />
</conditional>
<param name="adv.fix_omega" value="0" />
<param name="adv.omega" value="0.2" />
<param name="adv|fix_omega" value="0" />
<param name="adv|omega" value="0.2" />
<param name="RateAncestor" value="1" />
<param name="concat_nuc" ftype="fasta" value="concat.fasta" />
<param name="tree" value="RAxML_bestTree" ftype="nhx" />
<output name="2ngdn" value="1_2ngdn" />
<output name="2ngds" value="1_2ngds" />
<output name="2ngt" value="1_2ngt" />
<output name="twongdn" value="1_2ngdn" />
<output name="twongds" value="1_2ngds" />
<output name="twongt" value="1_2ngt" />
<output name="run">
<assert_contents>
<has_text text="CODONML (in paml version 4.9, March 2015)"/>
Expand All @@ -279,19 +279,19 @@ codeml '$codeml_ctl'
</output>
<output name="ctl" value="1_codeml.ctl" lines_diff="4" />
</test>
<test>
<test expect_num_outputs="9">
<conditional name="compat_model" >
<param name="brmodel" value="2" />
<param name="NSsites" value="0" />
</conditional>
<param name="adv.fix_omega" value="0" />
<param name="adv.omega" value="0.2" />
<param name="adv|fix_omega" value="0" />
<param name="adv|omega" value="0.2" />
<param name="RateAncestor" value="1" />
<param name="concat_nuc" ftype="fasta" value="concat.fasta" />
<param name="tree" value="tree_model2" ftype="nhx" />
<output name="2ngdn" value="2_2ngdn" />
<output name="2ngds" value="2_2ngds" />
<output name="2ngt" value="2_2ngt" />
<output name="twongdn" value="2_2ngdn" />
<output name="twongds" value="2_2ngds" />
<output name="twongt" value="2_2ngt" />
<output name="run">
<assert_contents>
<has_text text="CODONML (in paml version 4.9, March 2015)"/>
Expand All @@ -300,19 +300,19 @@ codeml '$codeml_ctl'
</output>
<output name="ctl" value="2_codeml.ctl" lines_diff="4" />
</test>
<test>
<test expect_num_outputs="9">
<conditional name="compat_model" >
<param name="brmodel" value="3" />
<param name="NSsites" value="2" />
</conditional>
<param name="adv.fix_omega" value="0" />
<param name="adv.omega" value="0.2" />
<param name="adv|fix_omega" value="0" />
<param name="adv|omega" value="0.2" />
<param name="RateAncestor" value="1" />
<param name="concat_nuc" ftype="fasta" value="concat.fasta" />
<param name="tree" value="tree_model3" ftype="nhx" />
<output name="2ngdn" value="3_2ngdn" />
<output name="2ngds" value="3_2ngds" />
<output name="2ngt" value="3_2ngt" />
<output name="twongdn" value="3_2ngdn" />
<output name="twongds" value="3_2ngds" />
<output name="twongt" value="3_2ngt" />
<output name="run">
<assert_contents>
<has_text text="CODONML (in paml version 4.9, March 2015)"/>
Expand Down

0 comments on commit 6ecdbaa

Please sign in to comment.