Mercurial > repos > iuc > hyphy_relax
diff hyphy_relax.xml @ 25:a4c5dc437558 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author | iuc |
---|---|
date | Tue, 27 Apr 2021 18:03:51 +0000 |
parents | 801547975424 |
children | 3415a580926d |
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--- a/hyphy_relax.xml Tue Apr 20 19:55:48 2021 +0000 +++ b/hyphy_relax.xml Tue Apr 27 18:03:51 2021 +0000 @@ -1,11 +1,9 @@ <?xml version="1.0"?> -<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09"> +<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy1" profile="19.09"> <description>Detect relaxed selection in a codon-based phylogenetic framework</description> <macros> <import>macros.xml</import> - <token name="@OPERATION@">RELAX</token> - <token name="@operation@">relax</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @@ -13,42 +11,56 @@ export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" && hyphy relax --alignment ./$input_file - #if $input_nhx: - --tree ./input.nhx - #end if - --models '$analysisType' + @INPUT_TREE@ + --models '$models' --code '$gencodeid' - #if $treeAnnotations == "2": - --test TEST - --reference REFERENCE - #else: - --test TEST + --test '$test' + #if $reference: + --reference '$reference' #end if - > '$relax_log' ; - @CATCH_ERROR@ + @advanced_options@ + --output '$relax_output' + @ERRORS@ ]]></command> <inputs> <expand macro="inputs"/> <expand macro="gencode"/> - <param argument="--model" name="analysisType" type="select" label="Analysis Type" > + <param argument="--models" type="select" label="Analysis Type" > <option value="All">All</option> <option value="Minimal">Minimal</option> </param> - <param name="treeAnnotations" type="select" label="Tree Annotations" help = "Is there one or two sets of annotated branches in the Newick file?"> - <option value="1">TEST only</option> - <option value="2">TEST and REFERENCE</option> + <param argument="--test" type="text" value="Unlabeled branches" optional="false" label="Branches to use as the test set"> + <sanitizer invalid_char=""> + <valid initial="default" /> + </sanitizer> </param> + <param argument="--reference" type="text" optional="true" label="Branches to use as the reference set"> + <sanitizer invalid_char=""> + <valid initial="default" /> + </sanitizer> + </param> + <expand macro="srv" /> </inputs> <outputs> - <data name="relax_log" format="txt"/> <data name="relax_output" format="hyphy_results.json"/> + <expand macro="alternative_model_output" /> </outputs> <tests> <test> <param name="input_file" ftype="fasta" value="relax-in1.fa"/> <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/> + <param name="test" value="TEST" /> <output name="relax_output" file="relax-out1.json" compare="sim_size"/> </test> + <test> + <param name="input_file" ftype="nex" value="relax-in2.nex"/> + <param name="srv_options" value="specify" /> + <param name="save_alternative_model" value="true" /> + <param name="test" value="PR" /> + <param name="srv" value="Yes" /> + <output name="relax_output" file="relax-out2-1.json" compare="sim_size"/> + <output name="alternative_model" file="relax-out2-2.json" compare="sim_size"/> + </test> </tests> <help><![CDATA[ RELAX: a test for selection differences