Mercurial > repos > dfornika > snippy
diff snippy.xml @ 21:0e733df972b5 draft
planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
| author | dfornika |
|---|---|
| date | Tue, 12 Mar 2019 17:37:29 -0400 |
| parents | 3bbfe41787af |
| children | 0bf16c8aca73 |
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--- a/snippy.xml Fri Mar 08 20:46:56 2019 -0500 +++ b/snippy.xml Tue Mar 12 17:37:29 2019 -0400 @@ -30,7 +30,7 @@ --minfrac $adv.minfrac --minqual $adv.minqual #if $adv.rgid - --rgid '$advanced.rgid' + --rgid '$adv.rgid' #end if #if $adv.bwaopt --bwaopt '$advanced.bwaopt' @@ -56,12 +56,17 @@ #import re #if str( $fastq_input.fastq_input_selector ) == "paired" #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_collection" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name) #else #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier) #end if mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ && tar -czf out.tgz ${dir_name} + #if "outcon" in str($outputs) and $adv.rename_cons + && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa + #end if ]]></command> @@ -99,6 +104,7 @@ <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" /> <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" /> <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" /> + <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" /> </section> <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">