annotate bamToFastq.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools bamtofastq
$tags
-i '$input'
-fq '$output'
#if $fq2:
    -fq2 '$output2'
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
        <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
        <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
            help="Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
    </inputs>
    <outputs>
        <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
        <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
            <filter>fq2 is True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="srma_in3.bam" ftype="bam" />
            <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.

@REFERENCES@
    ]]></help>
    <expand macro="citations" />
</tool>