Mercurial > repos > greg > affy2vcf
changeset 0:a39ee5dae75e draft
Uploaded
author | greg |
---|---|
date | Wed, 03 Oct 2018 12:58:15 -0400 |
parents | |
children | c15d12a508e5 |
files | affy2vcf.xml |
diffstat | 1 files changed, 76 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affy2vcf.xml Wed Oct 03 12:58:15 2018 -0400 @@ -0,0 +1,76 @@ +<tool id="affr2vcf" name="Convert Affymetrix" version="1.9"> + <description>genotype calls and intensities to VCF</description> + <requirements> + <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +#set text_outputs_dir = 'text_outputs' +mkdir $text_outputs_dir && +bcftools +affy2vcf.so +-- fasta_ref '$fasta_ref' +--annot '$annot' +--snp-posteriors '$text_outputs_dir/snp_posteriors.txt' +--summary '$text_outputs_dir/summary.txt' +--report '$text_outputs_dir/report.txt' +--calls '$text_outputs_dir/calls.txt' +--confidences '$text_outputs_dir/confidences.txt' +if str($output_gender_estimate_cond.output_gender_estimate) == "yes" + --sex '$text_outputs_dir/gender_estimate.txt' +#end if +#if str($append_version) == "no": + --no-version +#end if +--output '$output' +--output_type $output_type +--threads \${GALAXY_SLOTS:-4} + ]]></command> + <inputs> + <param name="fasta_ref" type="data" format="fasta" label="Fasta reference sequence" /> + <param name="annot" type="data" format="csv" label="Probeset annotation file" /> + <conditional name="output_gender_estimate_cond"> + <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"/> + </conditional> + <conditional name="append_version_cond"> + <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no" /> + <when value="yes"/> + </conditional> + </inputs> + <outputs> + <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}"> + <discover_datasets pattern="__name__" directory="output" format="txt" /> + </collection> + <data name="output" format="vcf" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +This tool converts Affymetrix genotype calls and intensity files to VCF format. + +----- + +**Required options** + +**Other options** + </help> + <citations> + <citation type="bibtex"> + @misc{None, + journal = {None}, + author = {Genovese, Giulio}, + title = {None}, + year = {None}, + url = {https://github.com/freeseek/gtc2vcf},} + </citation> + </citations> +</tool>