UrQt.xml

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    Copyright (C) 2015 Laurent Modolo

    This file is part of TEtools suite for galaxy.

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<tool id="urqt" name="UrQt" version="1.0.18" hidden="false">
    <description>fastq quality trimming</description>
    <!-- <version_command>UrQt</version_command> -->
    <command>nice -10 ${__root_dir__}/tools/pi_galaxy/UrQt
        --m 4
        --in ${input_file}
        --out ${output_file}
        --t ${threshold}
        #if $trimming.condition == "polyN":
            --N ${trimming.poly}
        #end if
        --pos ${pos}
        #if $empty_reads == "keep":
          --r
        #end if
        --min_read_size ${min_read_size}
        --v
        #if $is_paired_end.condition == "paired_end":
             --inpair ${is_paired_end.input_file_pair}
             --outpair ${output_file_pair}
        #end if
    </command>

    <inputs>
        <param name="input_file" type="data" format="fastq" label="input fastq file" />
        <conditional name="is_paired_end">
            <!-- <param name="condition" type="boolean" checked="false" truevalue="paired_end" falsevalue="single_end" label="paired-end data"/> -->
            <param name="condition" type="select" label="paired-end data">
                <option value="single_end">no</option>
                <option value="paired_end">yes</option>
            </param>
            <when value="single_end" />
            <when value="paired_end">
                <param name="input_file_pair" type="data" format="fastq" label="input fastq file for paired end data" />
            </when>
        </conditional>
        <param name="threshold" type="integer" value="20" min="0" max="45" label="minimum phred score for a ``informative quality'' (default: 20)"/>
        <param name="pos" type="select" label="expected position of trimmed sequence in the read (default: both)" value="both">
            <option value="both">trim at head and tail</option>
            <option value="head">trim at head</option>
            <option value="tail">trim at tail</option>
        </param>
        <conditional name="trimming">
            <!-- <param name="condition" type="boolean" checked="true" truevalue="quality" falsevalue="polyN" label="quality trimming"/> -->
            <param name="condition" type="select" label="type of trimming">
                <option value="quality">quality trimming</option>
                <option value="polyN">polyN</option>
            </param>
            <when value="quality" />
            <when value="polyN">
              <param name="poly" type="select" label="polyN to trim">
                <option value="A">polyA trimming</option>
                <option value="G">polyT trimming</option>
                <option value="G">polyG trimming</option>
                <option value="C">polyC trimming</option>
              </param>
            </when>
        </conditional>
        <param name="empty_reads" type="boolean" checked="true" truevalue="remove" falsevalue="keep" label="removing of empty reads (100% of bases trimmed) (default: the empty reads are removed from the output)"/>
        <param name="min_read_size" type="integer" value="0" min="0" label="remove all reads smaller than this size after the trimming step (default: 0)"/>
    </inputs>

    <outputs>
        <data format="fastq" name="output_file" label="${tool.name} on ${on_string}: trimmed fastq file"/>
        <data format="fastq" name="output_file_pair" label="${tool.name} on ${on_string}: trimmed fastq pair file">
            <filter>(is_paired_end['condition'] == 'paired_end')</filter>
        </data>
    </outputs>

    <help>
        Trim fastq reads according to a quality threshold using the UrQt software
        In the case of polyN trimming UrQt removes homopolymer of A/T/C/G at the end of the reads

        More information about UrQt available at: https://lbbe.univ-lyon1.fr/-UrQt-.html
    </help>
</tool>