view bam2roi.xml @ 0:61d9bdb6d519 draft

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<?xml version="1.0" encoding="UTF-8"?>
<tool id="bam2roi" name="BAM to ROI">
    <command>
    bam2roi
    $bam2roi_verbosity
    $bam2roi_strand_specific
    $bam2roi_ignore_pairing
    $bam2roi_link_over_skipped
    --input-file $bam2roi_input_file
    --output-file $bam2roi_output_file
    </command>

    <description>Create ROI from BAM file.</description>
    
    <!--
      Input Files and Parameters
    -->
    <inputs>
        <param name="bam2roi_input_file" type="data" format="sam,bam"
               label="Input File"
               help="SAM/BAM formatted file.  Must be sorted by coordinate." />

        <param name="bam2roi_ignore_pairing" type="boolean" falsevalue="" truevalue="--ignore-pairing"
               label="Ignore paired information"
               help="By default, a whole fragment/template extends a ROI for paired-end data.  When selected, reads are treated as in the single-end case." />
        <param name="bam2roi_link_over_skipped" type="boolean" falsevalue="" truevalue="--link-over-skipped"
               label="Link over skipped bases"
               help="When selected, a ROI continues over skipped bases." />
        <param name="bam2roi_strand_specific" type="boolean" falsevalue="" truevalue="--strand-specific"
               label="Compute strand-specific ROIs"
               label="When selected, the strands of the reads alignments are considered, e.g. there can be two or more ROIs on different strands that would overlap on the same strand." />

        <param name="bam2roi_verbosity" type="select" label="Verbosity" force_select="true" />
            <option value="" selected="true">normal</option>
            <option value="--verbose">verbose</option>
            <option value="--very-verbose">very verbose</option>
        </param>
    </inputs>
    
    <!--
      Output Files
    -->
    <outputs>
        <data label="${bam2roi_input_file.name}.roi" name="bam2roi_output_file" format="roi" />
    </outputs>

    <!--
      Recognize errors by return code and not output to stderr.
    -->
    <stdio>
        <exit_code range="1:" level="fatal" />
        <exit_code range=":-1" level="fatal" />
    </stdio>

    <!--
      Tool Help
    -->
    <help>No help yet.</help>
</tool>