view biotradis_remove_tags.xml @ 0:f47f5ba2c9be draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 3ea7f0b0c83b2e404a61d5c50545fe4b3bd2d6c6-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_tags -f $input_bam -t $tag -m $mismatches -o removed -v > $log

    ]]></command>
    <inputs>
         <param name="input_fastq" type="data" format="fastq" label="Fastq file" help="" />
         <param name="tag" type="text" label="Tags to remove" help="" />
         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
    </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>

</tool>