comparison macros.xml @ 4:85b3dc9b6830 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"

3:f6e3a10a88e5

<macros>
    <token name="@VERSION@">0.14.1.2</token>
    <token name="@GALAXY_VERSION@">galaxy0</token>
    <token name="@IDX_VERSION@">q6</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="0.14.1">salmon</requirement>
            <requirement type="package" version="1.10">samtools</requirement>
            <requirement type="package" version="0.2.0">vpolo</requirement>
            <requirement type="package" version="0.25.1">pandas</requirement>
            <requirement type="package" version="1.3.1">scipy</requirement>
        </requirements>
    </xml>
    <xml name="stranded">
        <param name="strandedness" type="select" label="Specify the strandedness of the reads">
                <option value="U" selected="True">Not stranded (U)</option>

        #if $geneMap:
            ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
        #end if

        salmon quant
            --index $index_path
            #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
                --libType ${quant_type.input.single_or_paired.strandedness}
                #if $compressed == 'GZ':
                    --unmatedReads <(zcat < ./single.$ext)
                #else if $compressed == 'BZ2':

4:85b3dc9b6830

<macros>
    <token name="@VERSION@">1.3.0</token>
    <token name="@GALAXY_VERSION@">galaxy0</token>
    <token name="@IDX_VERSION@">q7</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">salmon</requirement>
            <requirement type="package" version="1.3">seqtk</requirement>
            <requirement type="package" version="1.10">samtools</requirement>
            <requirement type="package" version="0.2.0">vpolo</requirement>
            <requirement type="package" version="1.0.3">pandas</requirement>
            <requirement type="package" version="1.4.1">scipy</requirement>
        </requirements>
    </xml>
    <xml name="stranded">
        <param name="strandedness" type="select" label="Specify the strandedness of the reads">
                <option value="U" selected="True">Not stranded (U)</option>

        #if $geneMap:
            ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
        #end if

        salmon quant
            --index '$index_path'
            #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
                --libType ${quant_type.input.single_or_paired.strandedness}
                #if $compressed == 'GZ':
                    --unmatedReads <(zcat < ./single.$ext)
                #else if $compressed == 'BZ2':