view bam_to_psl.xml @ 0:b6794f4cb1c6 draft default tip

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<tool id="bam_to_psl" name="Convert BAM to PSL format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
  <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#if $input.ext == 'bam':
    samtools view -o 'input.sam' -h '$input' &&
#else:
    ln -s '$input' 'input.sam' &&
#end if
python '${__tool_directory__}/bam_to_psl.py' 
--input_file 'input.sam'
--output_file '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam,sam" label="BAM or SAM file"/>
    </inputs>
    <outputs>
        <data name="output" format="psl"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input_1.sam" ftype="sam"/>
            <output name="output" value="output_1.psl" ftype="psl" compare="contains"/>
        </test>
        <test>
            <param name="input" value="input_2.bam" ftype="bam"/>
            <output name="output" value="output_2.psl" ftype="psl" compare="contains"/>
        </test>
    </tests>
    <help>
**What it does**

Converts a BAM or SAM dataset to PSL format - https://genome.ucsc.edu/FAQ/FAQformat.html#format2.
    </help>
    <expand macro="citations"/>
</tool>