Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites
changeset 3:bb483baa0e50 draft
Uploaded
author | greg |
---|---|
date | Wed, 22 Nov 2023 19:41:49 +0000 (13 months ago) |
parents | b64c03573271 |
children | 36e984464e12 |
files | cfsan_snp_pipeline_merge_sites.xml macros.xml |
diffstat | 2 files changed, 4 insertions(+), 28 deletions(-) [+] |
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--- a/cfsan_snp_pipeline_merge_sites.xml Wed Nov 22 17:59:10 2023 +0000 +++ b/cfsan_snp_pipeline_merge_sites.xml Wed Nov 22 19:41:49 2023 +0000 @@ -6,30 +6,20 @@ <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/snp_wind.py' ./ -#if str($input_type_cond.input_type) == 'single': - -n '$input_type_cond.input_vcf.element_identifier' - -f '$input_type_cond.input_vcf' -#else: - #for $input_vcf in $input_type_cond.input_vcf_collection: - -n '$input_vcf.element_identifier' - -f '$input_vcf' - #end for -#end if +#for $input_vcf in $input_vcf_collection: + -n '$input_vcf.element_identifier' -f '$input_vcf' +#end for -p 'var.fit.vcf' > ./file && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output' ]]></command> <inputs> - <expand macro="input_type_cond"/> + <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> </inputs> <outputs> <data name="output" format="tabular"/> </outputs> <tests> <test> - <param name="input_vcf" value="input1.vcf"/> - <output name="output" value="output.tabular"/> - </test> - <test> <param name="input_type" value="collection"/> <param name="input_vcf_collection"> <collection type="list">
--- a/macros.xml Wed Nov 22 17:59:10 2023 +0000 +++ b/macros.xml Wed Nov 22 19:41:49 2023 +0000 @@ -8,20 +8,6 @@ <requirement type="package" version="3.6.8">python</requirement> </requirements> </xml> - <xml name="input_type_cond"> - <conditional name="input_type_cond"> - <param name="input_type" type="select" label="Choose the category for the files to be analyzed"> - <option value="single" selected="true">Single files</option> - <option value="collection">Collection of files</option> - </param> - <when value="single"> - <param name="input_vcf" type="data" format="vcf" label="VCF file"/> - </when> - <when value="collection"> - <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> - </when> - </conditional> - </xml> <xml name="citations"> <citations> <citation type="doi">10.7717/peerj-cs.20</citation>