annotate biotradis_filter_tags.xml @ 2:0cfaf8b3049f draft

Deleted selected files

<tool id="filter_tradis_tags" name="filter tradis tags" version="@VERSION@">
    <description>Filters a BAM file and outputs reads with tag matching -t option.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
    
    filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered

    ]]></command>
    <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
         <param name="tag" type="text" label="Tags to filter" help="" />
         <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" />
         <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
    </inputs>

    <outputs>
       <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.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>