Mercurial > repos > rdvelazquez > hyphy_relax
diff hyphy_relax.xml @ 0:a9f460ad3ffe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'17327d46ff082448f0a0fc3b6827f5d9d6124a10\n'-dirty
| author | rdvelazquez |
|---|---|
| date | Tue, 08 Jan 2019 10:40:23 -0500 |
| parents | |
| children | f078fc88982d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_relax.xml Tue Jan 08 10:40:23 2019 -0500 @@ -0,0 +1,78 @@ +<?xml version="1.0"?> +<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0"> + <description>Detect relaxed selection in a codon-based phylogenetic framework</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>HYPHYMP --version | tail -n 1 | awk '{print $1}'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + #if $treeAnnotations == 1: + ln -s '$input_file' relax_input.fa && + ln -s '$input_nhx' relax_input.nhx && + echo $gencodeid > tool_params && + echo `pwd`/relax_input.fa >> tool_params && + echo `pwd`/relax_input.nhx >> tool_params && + echo 3 && + echo 2 && + echo $analysisType > tool_params && + @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' + #else: + ln -s '$input_file' relax_input.fa && + ln -s '$input_nhx' relax_input.nhx && + echo $gencodeid > tool_params && + echo `pwd`/relax_input.fa >> tool_params && + echo `pwd`/relax_input.nhx >> tool_params && + echo 2 && + echo $analysisType > tool_params && + @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' + #end if + ]]> + </command> + <inputs> + <param name="input_file" type="data" format="fasta" label="Input FASTA file" /> + <param name="input_nhx" type="data" format="nhx" label="Input newick file" /> + <param name="gencodeid" type="select" label="Genetic code"> + <option value="1">Universal code</option> + <option value="2">Vertebrate mitochondrial DNA code</option> + <option value="3">Yeast mitochondrial DNA code</option> + <option value="4">Mold, Protozoan and Coelenterate mt; Mycloplasma/Spiroplasma</option> + <option value="5">Invertebrate mitochondrial DNA code</option> + <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear code</option> + <option value="7">Echinoderm mitochondrial DNA code</option> + <option value="8">Euplotid Nuclear code</option> + <option value="9">Alternative Yeast Nuclear code</option> + <option value="10">Ascidian mitochondrial DNA code</option> + <option value="11">Flatworm mitochondrial DNA code</option> + <option value="12">Blepharisma Nuclear code</option> + </param> + <param name="analysisType" type="select" label="Analysis Type"> + <option value="1">All</option> + <option value="2">Minimal</option> + </param> + <param name="treeAnnotations" type="select" label="Tree Annotations"> + <option value="1">TEST only</option> + <option value="2">TEST and REFERENCE</option> + </param> + </inputs> + <outputs> + <data name="relax_log" format="txt" /> + <data name="relax_output" format="json" from_work_dir="relax_input.fa.RELAX.json" /> + </outputs> + <tests> + <test> + <param name="input_file" ftype="fasta" value="relax-in1.fa" /> + <param name="input_nhx" ftype="nhx" value="relax-in1.nhx" /> + <output name="relax_output" file="relax-out1.json" compare="sim_size" /> + </test> + </tests> + <help> + <![CDATA[ +RELAX (Detect relaxed selection in a codon-based phylogenetic framework) + ]]> + </help> + <expand macro="citations"> + <citation type="doi">10.1093/molbev/msv022</citation> + </expand> +</tool>