comparison hyphy_meme.xml @ 2:b15d64d85c03 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"

1:d02c8e6f7f2a

<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
    <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 &&
        @HYPHY_INVOCATION@ meme
            --alignment ./meme_input.fa
            --tree ./meme_input.nhx
            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            > '$meme_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 threshold"/>
    </inputs>
    <outputs>
        <data name="meme_log" format="txt"/>
        <data name="meme_output" format="hyphy_results.json" from_work_dir="meme_input.fa.MEME.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>

2:b15d64d85c03

<?xml version="1.0"?>
<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1">
    <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'
    ]]></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>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>