comparison fasterq_dump.xml @ 30:4317d3cb6cba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 173bdd37f6353cd869526d193e8d06038ae12787

29:6ea73833cf67

    @COPY_CONFIGFILE@
    @CONFIGURE_RETRY@
    @SET_ACCESSIONS@
    while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
        --seq-defline '@\$sn/\$ri'
        --qual-defline '+'
        $adv.split
        #if str( $adv.minlen ) != "":
            --min-read-len "$adv.minlen"
        #end if

    </command>
    <expand macro="configfile_hack"/>
    <inputs>
        <expand macro="input_conditional"/>
        <section name="adv" title="Advanced Options" expanded="False">
            <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
            <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
                <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
                <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
                <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>

30:4317d3cb6cba

    @COPY_CONFIGFILE@
    @CONFIGURE_RETRY@
    @SET_ACCESSIONS@
    while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
        --seq-defline '$adv.seq_defline'
        --qual-defline '+'
        $adv.split
        #if str( $adv.minlen ) != "":
            --min-read-len "$adv.minlen"
        #end if

    </command>
    <expand macro="configfile_hack"/>
    <inputs>
        <expand macro="input_conditional"/>
        <section name="adv" title="Advanced Options" expanded="False">
            <expand macro="defline" defline_param="--seq-defline" defline_default="@$sn/$ri"/>
            <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
            <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
                <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
                <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
                <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>