# HG changeset patch # User iuc # Date 1580179809 0 # Node ID a3f95a688c4702fb9dc6415707a6b39b91906768 # Parent 43791d945de1d80ceebbb7b9953d6275418d6dde "planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792" diff -r 43791d945de1 -r a3f95a688c47 snippy-core.xml --- a/snippy-core.xml Sun Dec 01 18:05:33 2019 +0000 +++ b/snippy-core.xml Tue Jan 28 02:50:09 2020 +0000 @@ -1,5 +1,5 @@ - + Combine multiple Snippy outputs into a core SNP alignment @@ -9,14 +9,14 @@ diff -r 43791d945de1 -r a3f95a688c47 snippy.xml --- a/snippy.xml Sun Dec 01 18:05:33 2019 +0000 +++ b/snippy.xml Tue Jan 28 02:50:09 2020 +0000 @@ -1,4 +1,4 @@ - + Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. @@ -12,8 +12,19 @@ @REFERENCE_SOURCE_FILE@ + #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) + #elif str( $fastq_input.fastq_input_selector ) == "single" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) + #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" + #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) + #end if + snippy - --outdir 'out' + --outdir '${dir_name}' --cpus \${GALAXY_SLOTS:-1} --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024)) @REFERENCE_COMMAND@ @@ -40,26 +51,12 @@ --peil '$fastq_input.fastq_input_interleaved' #end if - && - - #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) - #elif str( $fastq_input.fastq_input_selector ) == "single" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier) - #elif str( $fastq_input.fastq_input_selector ) == "paired_iv" - #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier) + #if "outcon" in str($outputs) and $adv.rename_cons + && sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa' #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 - - + && cp -r '${dir_name}' out + && tar -czf out.tgz '${dir_name}' ]]>