Mercurial > repos > iuc > bcftools_annotate
changeset 10:365022dae1c9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 942ca2971ae6a72e548fde6186c6408a1e236653
| author | iuc |
|---|---|
| date | Mon, 29 Jul 2019 17:52:55 -0400 |
| parents | 9f281310c048 |
| children | 0ba50f5955b6 |
| files | bcftools_annotate.xml test-data/annots.bcf |
| diffstat | 2 files changed, 28 insertions(+), 5 deletions(-) [+] |
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--- a/bcftools_annotate.xml Wed Jun 05 12:45:20 2019 -0400 +++ b/bcftools_annotate.xml Mon Jul 29 17:52:55 2019 -0400 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2"> <description>Annotate and edit VCF/BCF files</description> <macros> <token name="@EXECUTABLE@">annotate</token> @@ -14,9 +14,19 @@ #set $annotation_hdr = None #set $section = $sec_annofile #if $section.annofile.anno_fmt == 'vcf': - #set $annotation_file = 'annotations.vcf.gz' - bgzip -c "$section.annofile.annotations" > $annotation_file && - bcftools index $annotation_file && + #if $section.annofile.annotations.is_of_type('vcf') + #set $annotation_file = 'annotations.vcf.gz' + bgzip -c "$section.annofile.annotations" > $annotation_file && + bcftools index $annotation_file && + #elif $section.annofile.annotations.is_of_type('bcf') + #set $annotation_file = 'annotations.bcf' + ln -s '$section.annofile.annotations' $annotation_file && + #if $section.annofile.annotations.metadata.bcf_index: + ln -s '${section.annofile.annotations.metadata.bcf_index}' ${annotation_file}.csi && + #else + bcftools index $annotation_file && + #end if + #end if #elif $section.annofile.anno_fmt == 'tab': #if $section.annofile.annotations.is_of_type('bed') #set $annotation_file = 'annotations.bed.gz' @@ -97,7 +107,7 @@ </param> <when value="none"/> <when value="vcf"> - <param name="annotations" type="data" format="vcf" label="Annotations VCF"/> + <param name="annotations" type="data" format="vcf,bcf" label="Annotations VCF"/> </when> <when value="tab"> <param name="annotations" type="data" format="tabular,bed" label="Annotations"> @@ -196,6 +206,19 @@ </output> </test> <test> + <param name="input_file" ftype="vcf" value="annotate.vcf" /> + <param name="anno_fmt" value="vcf" /> + <param name="annotations" value="annots.bcf" /> + <param name="columns" value="STR,ID,QUAL,FILTER" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="idIndel" /> + <has_text text="STR=testSNP" /> + </assert_contents> + </output> + </test> + <test> <param name="input_file" ftype="vcf" value="annotate2.vcf" /> <param name="anno_fmt" value="vcf" /> <param name="annotations" value="annots2.vcf" />