comparison sRbowtie.xml @ 3:61ab0d4bd187 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 7e91a34b0ebd7bc284823c71f32691170183e388

2:304adcfe3660

<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.2">
    <description>for small RNA short reads</description>
    <requirements>
        <requirement type="package" version="1.1.2=py27_0">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>

            ln -s -f '$refGenomeSource.ownFile' genome.fa &&
            #set index_path = 'genome'
        #else:
            #set index_path = $refGenomeSource.index.fields.path
        #end if
        #if $input.extension == "fasta":
            #set format = "-f"
        #elif $input.extension == "fastq" or $input.extension == "fastqsanger":
            #set format = "-q"
        #end if

        ## set the method_prefix
        #if $method == "RNA":

3:61ab0d4bd187

<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.3">
    <description>for small RNA short reads</description>
    <requirements>
        <requirement type="package" version="1.1.2=py27_0">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>

            ln -s -f '$refGenomeSource.ownFile' genome.fa &&
            #set index_path = 'genome'
        #else:
            #set index_path = $refGenomeSource.index.fields.path
        #end if
        #if $input.is_of_type('fasta'):
            #set format = "-f"
        #elif $input.is_of_type('fastq'):
            #set format = "-q"
        #end if

        ## set the method_prefix
        #if $method == "RNA":