view labels.xml @ 0:1e495837e8d3 draft

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<?xml version="1.0"?>
<tool name="labels" id="bg_labels" version="1.0.5.0">
    <description>remapper and annotator of alignments</description>
    <requirements>
        <requirement type="package" version="1.0.5">labels</requirement>
        <requirement type="package" version="0.7.7">pysam</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
<![CDATA[
        pylapels
            -c "${chrom_list}"
            $alias
            $sorted
            -p \${GALAXY_SLOTS:-4}
            -q
            -o $output
            $input_mod
            $input_bam
]]>
    </command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="BAM file">
            <validator type="unspecified_build" />
            <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
        </param>
        <param name="input_mod" type="data" format="txt" label="MOD file">

        <param name="alias" optional="true" type="data" format="tabular" label="CSV? file for alias classes of sequence name"/> 
        <param name="sorted" type="boolean" truevalue="-n" falsevalue="" 
            label="Sort the output BAM file by read names" help="-n"/>
        <param name="chrom_list" type="text" value="all" label="Comma-separated list of chromosomes in the output" help="e.g. 1,2,3 (-c)" />

    </inputs>
    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>

    </tests>
    <help>
<![CDATA[

**What it does**

A remapper and annotator of in silico (pseudo) genome alignments.

 https://code.google.com/p/lapels/

]]>
</help>
</tool>