annotate pindel2vcf.xml @ 0:f8f8dbf89999 draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty

<tool id="pindel2vcf" name="Pindel2Vcf" version="0.6.3">
    <description>convert Pindel to VCF and index</description>
    <requirements>
        <requirement type="package" version="0.2.5b8">pindel</requirement>
        <requirement type="package" version="0.2.3.48">igvtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command><![CDATA[
    pindel2vcf
    -p "$input_file"
    -r "$reference"
    -R "$official_reference_name"
    -d 00000000
    -v "$input_file".vcf &&
    mv "$input_file".vcf "$vcf_file"
]]></command>
    <inputs>
        <param name="input_file" type="data" format="txt" label="File to be converted"/>
        <param name="reference" format="fasta" type="data" label="Reference genome in fasta format"/>
        <param name="official_reference_name" type="text" label="Official Name for Reference Genome"/>
    </inputs>
    <outputs>
        <data name="vcf_file" type="tabular" format="vcf" label="${input_file.name}.vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="X_Hum1_D" ftype="txt"/>
            <param name="reference" value="dm6.fa" ftype="fasta"/>
            <param name="official_reference_name" value="dmel_r6.10_FB2016_02" ftype="text"/>
            <output name="vcf_file" file="X_Hum1_D.vcf" ftype="vcf"/>
        </test>
    </tests>
    <help>
        This tool converts Pindel output files to VCF format.
        The following inputs are required:
        - File(s) to be converted
        - Reference genome in fasta format
        - Official Name for Reference genome
        - Date the reference genome was created
    </help>
    <citations>
        <citation type="doi">doi:10.1093/bioinformatics/btp394</citation>
    </citations>
</tool>