comparison hyphy_relax.xml @ 23:801547975424 draft

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

22:91e47cb67709

<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09">
    <description>Detect relaxed selection in a codon-based
    phylogenetic framework</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input_file' relax_input.fa &&
        ln -s '$input_nhx' relax_input.nhx &&

        export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
        hyphy relax
            --alignment ./relax_input.fa
            --tree ./relax_input.nhx
            --models '$analysisType'
            --code '$gencodeid'
            #if $treeAnnotations == "2":
                --test TEST
                --reference REFERENCE
            #else:
                --test TEST
            #end if
            > '$relax_log'
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param argument="--model" name="analysisType" type="select" label="Analysis Type" >

            <option value="2">TEST and REFERENCE</option>
        </param>
    </inputs>
    <outputs>
        <data name="relax_log" format="txt"/>
        <data name="relax_output" format="hyphy_results.json" 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"/>

23:801547975424

<tool id="hyphy_relax" name="HyPhy-RELAX" version="@VERSION@+galaxy0" profile="19.09">
    <description>Detect relaxed selection in a codon-based
    phylogenetic framework</description>
    <macros>
        <import>macros.xml</import>
        <token name="@OPERATION@">RELAX</token>
        <token name="@operation@">relax</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @SYMLINK_FILES@
        export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
        hyphy relax
            --alignment ./$input_file
            #if $input_nhx:
                --tree ./input.nhx
            #end if
            --models '$analysisType'
            --code '$gencodeid'
            #if $treeAnnotations == "2":
                --test TEST
                --reference REFERENCE
            #else:
                --test TEST
            #end if
            > '$relax_log' ;
        @CATCH_ERROR@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <param argument="--model" name="analysisType" type="select" label="Analysis Type" >

            <option value="2">TEST and REFERENCE</option>
        </param>
    </inputs>
    <outputs>
        <data name="relax_log" format="txt"/>
        <data name="relax_output" format="hyphy_results.json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="relax-in1.fa"/>
            <param name="input_nhx" ftype="nhx" value="relax-in1.nhx"/>