Mercurial > repos > iuc > hyphy_fel
diff hyphy_fel.xml @ 1:6c3ece5fb602 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
author | iuc |
---|---|
date | Wed, 21 Aug 2019 12:27:42 -0400 |
parents | 24a2bf70dbdd |
children | a8b34daec0d9 |
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--- a/hyphy_fel.xml Thu Jan 17 04:23:36 2019 -0500 +++ b/hyphy_fel.xml Wed Aug 21 12:27:42 2019 -0400 @@ -4,47 +4,43 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> - <command detect_errors="exit_code"> - <![CDATA[ - ln -s '$input_file' fel_input.fa && - ln -s '$input_nhx' fel_input.nhx && - echo $gencodeid > tool_params && - echo `pwd`/fel_input.fa >> tool_params && - echo `pwd`/fel_input.nhx >> tool_params && - echo '$branches' >> tool_params && - echo '$include_srv' >> tool_params && - echo '$p_value' >> tool_params && - @HYPHY_INVOCATION@ \$HYPHY_LIB/TemplateBatchFiles/SelectionAnalyses/FEL.bf > '$fel_log' - ]]> - </command> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_file' fel_input.fa && + ln -s '$input_nhx' fel_input.nhx && + @HYPHY_INVOCATION@ fel + --alignment ./fel_input.fa + --tree ./fel_input.nhx + --code '$gencodeid' + --branches '$branches' + --srv '$include_srv' + --pvalue '$p_value' + > '$fel_log' + ]]></command> <inputs> - <expand macro="inputs" /> - <expand macro="gencode" /> - <expand macro="branches" /> - <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value" /> + <expand macro="inputs"/> + <expand macro="gencode"/> + <expand macro="branches"/> + <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value"/> <param name="include_srv" type="select" label="Include synonymous rate variation"> - <option value="1">Yes (recommended)</option> - <option value="2">No</option> + <option value="Yes">Yes (recommended)</option> + <option value="No">No</option> </param> </inputs> <outputs> - <data name="fel_log" format="txt" /> - <data name="fel_output" format="json" from_work_dir="fel_input.fa.FEL.json" /> + <data name="fel_log" format="txt"/> + <data name="fel_output" format="hyphy_results.json" from_work_dir="fel_input.fa.FEL.json"/> </outputs> <tests> <test> - <param name="input_file" ftype="fasta" value="absrel-in1.fa" /> - <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx" /> - <output name="fel_output" file="fel-out1.json" compare="sim_size" /> + <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> + <output name="fel_output" file="fel-out1.json" compare="sim_size"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ FEL (Fixed Effects Likelihood) uses a maximum-likelihood (ML) approach to infer nonsynoymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny. This method assumes that the selection pressure for each site is constant along the entire phylogeny. - ]]> - </help> + ]]></help> <expand macro="citations"> <citation type="doi">10.1093/molbev/msi105</citation> </expand>