Mercurial > repos > rdvelazquez > hyphy_relax
view hyphy_relax.xml @ 3:0648b03f1d2f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit b'66899249856184fad03efcca5d444084d78eac83\n'-dirty
author | rdvelazquez |
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date | Mon, 11 Feb 2019 20:18:43 -0500 |
parents | f078fc88982d |
children | 7782bb7bc7b7 |
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<?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" /> <expand macro="version_command" /> <command detect_errors="exit_code"> <![CDATA[ #if $treeAnnotations == 2: ln -s '$input_file' relax_input.fa && ln -s '$input_nhx' relax_input.nhx && echo $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && echo '$treeAnnotations' >> 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 $gencodeid > tool_params && echo `pwd`/relax_input.fa >> tool_params && echo `pwd`/relax_input.nhx >> tool_params && echo '$treeAnnotations' >> tool_params && echo '2' && echo '$analysisType' >> tool_params && @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/RELAX.bf > '$relax_log' #end if ]]> </command> <inputs> <expand macro="inputs" /> <expand macro="gencode" /> <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="hyphy_json_results" 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/msu400</citation> </expand> </tool>