Mercurial > repos > greg > affy2vcf
changeset 12:c5fc0983b98c draft
Uploaded
author | greg |
---|---|
date | Fri, 12 Oct 2018 08:39:13 -0400 |
parents | 55f227ba9972 |
children | ea728b639a77 |
files | affy2vcf.xml |
diffstat | 1 files changed, 33 insertions(+), 15 deletions(-) [+] |
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--- a/affy2vcf.xml Thu Oct 11 14:24:46 2018 -0400 +++ b/affy2vcf.xml Fri Oct 12 08:39:13 2018 -0400 @@ -14,13 +14,13 @@ --fasta-ref '$reference_genome_source_cond.locally_cached_item' #end if --annot '$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) == "yes" - --sex '$text_outputs_dir/gender_estimate.txt' +--snp-posteriors '$snp_posteriors' +--summary '$summary' +--report '$report' +--calls '$calls' +--confidences '$confidences' +#if str($output_gender_estimate_cond.output_gender_estimate) == "yes" + --sex '$gender_estimate' #end if #if str($append_version) == "no": --no-version @@ -30,7 +30,6 @@ --threads \${GALAXY_SLOTS:-4} ]]></command> <inputs> - <param name="annot" type="data" format="csv" label="Probeset annotation file" /> <conditional name="reference_genome_source_cond"> <param name="reference_genome_source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?"> <option value="history" selected="true">Use a reference genome from my history</option> @@ -51,10 +50,20 @@ </param> </when> </conditional> - <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> + <param name="annot" type="data" format="csv" label="Probeset annotation file" /> + <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" /> + <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" /> + <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" /> + <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" /> + <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" /> + <conditional name="output_gender_estimate_cond"> + <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"/> + </conditional> <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> @@ -67,13 +76,22 @@ </param> </inputs> <outputs> - <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}"> - <discover_datasets pattern="__name__" directory="output" format="txt" /> - </collection> <data name="output" format="vcf" /> + <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}"> + <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter> + </data> </outputs> <tests> <test> + <param name="reference_genome_source" value="history"/> + <param name="history_item" value="GCF_000222465.1_Adig_1.1_genomic.fna" ftype="fasta"/> + <param name="annot" value="annot.csv" ftype="csv"/> + <param name="summary" value="summary.txt" ftype="txt"/> + <param name="snp_posteriors" value="snp_posteriors.txt" ftype="txt"/> + <param name="report" value="report.txt" ftype="txt"/> + <param name="confidences" value="confidences.txt" ftype="txt"/> + <param name="calls" value="calls.txt" ftype="txt"/> + <output name="output" value="output.vcf" ftype="vcf"/> </test> </tests> <help>