view biotradis_remove_tags.xml @ 8:9b1daaba9e8d draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 44b6f6a2bdcd4ba2dabc3d65c7feefcd2ff3b6db-dirty"

<tool id="remove_tradis_tags" name="remove tradis tags" version="@VERSION@">
    <description>Removes transposon sequence and quality tags from the read strings</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    
    remove_tradis_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log

    ]]>    </command>
    <inputs>
        <param name="input_fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Fastq file"/>
        <param name="tag" type="text" label="Tags to remove" />
        <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" />
    </inputs>

    <outputs>
        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log"/>
        <data name="filtered_tags" format="fastqsanger" label="${tool.name} on ${on_string}" from_work_dir="removed.rmtag.fatsq" />
    </outputs>

    <tests>
    </tests>
    <help><![CDATA[
        Adds transposon sequence and quality tags to the read strings and
        outputs a BAM.

        Usage: add_tags -b file.bam [options]

        Options:
        -b  : bam file with tradis tags
        -v  : verbose debugging output
    ]]>    </help>
    <expand macro="citations" />

</tool>