Mercurial > repos > portiahollyoak > pindel2vcf
diff pindel2vcf.xml @ 0:f8f8dbf89999 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty
| author | portiahollyoak |
|---|---|
| date | Tue, 17 May 2016 05:02:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pindel2vcf.xml Tue May 17 05:02:35 2016 -0400 @@ -0,0 +1,46 @@ +<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> \ No newline at end of file