annotate bam_to_sam.xml @ 5:f57df915aa10 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1">
    <description>convert BAM to SAM</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command><![CDATA[
        samtools view -o '${output1}' ${header} '${input1}'
    ]]></command>

    <inputs>
        <param format="bam" name="input1" type="data" label="BAM File to Convert" />
        <param name="header" label="Header options" type="select"
               help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
          <option value="-h">Include header in SAM output (-h)</option>
          <option value="-H">Return header only (-H)</option>
          <option value="">Exclude header</option>
        </param>
    </inputs>
    <outputs>
        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
    </outputs>
    <tests>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="-h" />
            <output file="bam_to_sam_out1.sam" name="output1" />
        </test>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="-H" />
            <output file="bam_to_sam_out2.sam" name="output1" />
        </test>
        <test>
            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
            <param name="header" value="" />
            <output file="bam_to_sam_out3.sam" name="output1" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Converts BAM dataset to SAM using the ``samtools view`` command.
    ]]></help>
    <expand macro="citations"/>
</tool>