Mercurial > repos > iuc > bcftools_gtcheck
diff bcftools_gtcheck.xml @ 5:9d243d49870f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author | iuc |
---|---|
date | Thu, 13 Apr 2017 17:43:41 -0400 |
parents | d8c55ac67d89 |
children | a1213a0b7b66 |
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--- a/bcftools_gtcheck.xml Sat Mar 11 17:59:29 2017 -0500 +++ b/bcftools_gtcheck.xml Thu Apr 13 17:43:41 2017 -0400 @@ -12,16 +12,17 @@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ +@PREPARE_REGIONS_FILE@ #set $section = $sec_default #set $genotypes_vcf = None #if $section.genotypes: #if $section.genotypes.is_of_type('vcf') #set $genotypes_vcf = 'genotypes.vcf.gz' - bgzip -c "$section.genotypes" > $genotypes_vcf && + bgzip -c '$section.genotypes' > $genotypes_vcf && bcftools index $genotypes_vcf && #elif $section.genotypes.is_of_type('bcf') #set $genotypes_vcf = 'genotypes.bcf' - ln -s "$ection.genotypes" $genotypes_vcf && + ln -s '$ection.genotypes' $genotypes_vcf && #if $section.genotypes.metadata.bcf_index: ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi && #else @@ -40,27 +41,27 @@ #end if #if $section.genotypes: - --genotypes "${section.genotypes}" + --genotypes '${section.genotypes}' #end if ${section.all_sites} #if $section.GTs_only: - --GTs-only "${section.GTs_only}" + --GTs-only '${section.GTs_only}' #end if ${section.homs_only} #if $section.plot: - --plot "${section.plot}" + --plot '${section.plot}' #end if #if $section.query_sample: - --query-sample "${section.query_sample}" + --query-sample '${section.query_sample}' #end if #if $section.target_sample: - --target-sample "${section.target_sample}" + --target-sample '${section.target_sample}' #end if #set $section = $sec_restrict @@ -70,7 +71,7 @@ ## Primary Input/Outputs @INPUT_FILE@ -> "$output_file" +> '$output_file' ]]> </command> <inputs> @@ -96,11 +97,10 @@ <tests> <test> <param name="input_file" ftype="vcf" value="view.vcf" /> - <param name="GTs_only" value="" /> + <param name="GTs_only" value="99" /> <output name="output_file"> <assert_contents> - <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/> - <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/> + <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/> </assert_contents> </output> </test>