Mercurial > repos > greg > affy2vcf
changeset 7:4dc497887a5c draft
Uploaded
author | greg |
---|---|
date | Fri, 05 Oct 2018 11:09:55 -0400 |
parents | 54dfcde738ad |
children | 192da25388ec |
files | affy2vcf.xml |
diffstat | 1 files changed, 25 insertions(+), 23 deletions(-) [+] |
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--- a/affy2vcf.xml Fri Oct 05 10:58:29 2018 -0400 +++ b/affy2vcf.xml Fri Oct 05 11:09:55 2018 -0400 @@ -7,17 +7,21 @@ #set text_outputs_dir = 'text_outputs' mkdir $text_outputs_dir && bcftools +affy2vcf.so ---fasta_ref '$reference_genome.fasta_ref' +#if str($reference_genome_source_cond.reference_genome_source) == "history": + --fasta_ref '$reference_genome_source_cond.history_item' +#else: + --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_cond.output_gender_estimate) == "yes" +#if str($output_gender_estimate) == "yes" --sex '$text_outputs_dir/gender_estimate.txt' #end if -#if str($append_version_cond.append_version) == "no": +#if str($append_version) == "no": --no-version #end if --output '$output' @@ -26,16 +30,16 @@ ]]></command> <inputs> <param name="annot" type="data" format="csv" label="Probeset annotation file" /> - <conditional name="reference_genome"> - <param name="source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?"> + <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> <option value="cached">Use a locally cached genome index</option> </param> <when value="history"> - <param name="fasta_ref" type="data" format="fasta" label="Select reference genome" /> + <param name="history_item" type="data" format="fasta" label="Select reference genome" /> </when> <when value="cached"> - <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence"> + <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence"> <options from_data_table="all_fasta"> <column name="name" index="1"/> <column name="value" index="2"/> @@ -46,22 +50,20 @@ </param> </when> </conditional> - <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> + <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="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> + <param name="output_type" type="select" force_select="true" label="Select format for output?"> + <option value="v" selected="true">Uncompressed VCF</option> + <option value="z">Compressed VCF</option> + <option value="u" selected="true">Uncompressed BCF</option> + <option value="b">Compressed BCF</option> + </param> </inputs> <outputs> <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">