Mercurial > repos > iuc > hyphy_fel
diff hyphy_fel.xml @ 33:8a6ef85b934d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
author | iuc |
---|---|
date | Wed, 30 Mar 2022 00:12:04 +0000 |
parents | fc50c4bac0a3 |
children | ec783806a5c3 |
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--- a/hyphy_fel.xml Sat Nov 27 11:31:22 2021 +0000 +++ b/hyphy_fel.xml Wed Mar 30 00:12:04 2022 +0000 @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09"> <description>Fixed Effects Likelihood</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @SYMLINK_FILES@ @@ -15,6 +15,9 @@ @branch_options@ --srv '$include_srv' --pvalue '$p_value' + @resample@ + --precision $precision + $ci --output '$fel_output' @ERRORS@ ]]></command> @@ -27,6 +30,12 @@ <option value="Yes">Yes (recommended)</option> <option value="No">No</option> </param> + <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" /> + <expand macro="resample"/> + <param argument="--precision" type="select" label="Optimization precision for preliminary fits"> + <option value="standard">Standard</option> + <option value="reduced">Reduced for faster fitting</option> + </param> </inputs> <outputs> <data name="fel_output" format="hyphy_results.json" /> @@ -37,6 +46,13 @@ <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> <output name="fel_output" file="fel-out1.json" compare="sim_size"/> </test> + <test> + <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> + <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> + <param name="ci" value="true" /> + <param name="precision" value="reduced" /> + <output name="fel_output" file="fel-out1.json" compare="sim_size"/> + </test> </tests> <help><![CDATA[ FEL : Fixed effects likelihood