comparison hyphy_meme.xml @ 23:2f07f5b4e47b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

22:24a21a467399

<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0" profile="19.09">
    <description>Mixed Effects Model of Evolution</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' meme_input.fa &&
        ln -s '$input_nhx' meme_input.nhx &&
        @HYPHYMPI@ meme
            --alignment ./meme_input.fa
            --tree ./meme_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            --output '$meme_output'
            > '$meme_log'
            ;
        @CATCH_MPIERR@
    ]]></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 threshold"/>
    </inputs>
    <outputs>
        <data name="meme_log" format="txt"/>
        <data name="meme_output" format="hyphy_results.json" />
    </outputs>

23:2f07f5b4e47b

<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09">
    <description>Mixed Effects Model of Evolution</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">MEME</token>
        <token name="@operation@">meme</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        @HYPHYMPI@ meme
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            --output '$meme_output'
            --full-model '$full_model'
            > '$meme_log'
            ;
        @CATCH_ERROR@
    ]]></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 threshold"/>
        <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
    </inputs>
    <outputs>
        <data name="meme_log" format="txt"/>
        <data name="meme_output" format="hyphy_results.json" />
    </outputs>