| Previous changeset 8:32f2211eeec3 (2019-12-01) Next changeset 10:3fe8ef358d66 (2020-01-30) |
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Commit message:
"planemo upload commit 02413e02c9484cdb604bda2c09931599f9259792" |
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modified:
snippy-core.xml snippy.xml |
| b |
| diff -r 32f2211eeec3 -r e4d0231d8595 snippy-core.xml --- a/snippy-core.xml Sun Dec 01 13:06:05 2019 -0500 +++ b/snippy-core.xml Mon Jan 27 21:50:49 2020 -0500 |
| [ |
| @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy1"> +<tool id="snippy_core" name="snippy-core" version="@VERSION@+galaxy2"> <description> Combine multiple Snippy outputs into a core SNP alignment </description> @@ -9,14 +9,14 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @REFERENCE_SOURCE_FILE@ + mkdir 'snippy_dirs' && cd 'snippy_dirs' && #for $indir in $indirs - #set $sample_name = os.path.splitext(os.path.basename(str($indir.name)))[0] - mkdir '$sample_name' && tar -xf '$indir' -C '$sample_name' --strip-components=1 && + tar -xf '$indir' -C . && #end for - #set snippy_dirs = " ".join(["'{0}'".format(os.path.splitext(os.path.basename(str($indir.name)))[0]) for $indir in $indirs]) + cd - && snippy-core @REFERENCE_COMMAND@ - ${snippy_dirs} + snippy_dirs/* ]]></command> <inputs> |
| b |
| diff -r 32f2211eeec3 -r e4d0231d8595 snippy.xml --- a/snippy.xml Sun Dec 01 13:06:05 2019 -0500 +++ b/snippy.xml Mon Jan 27 21:50:49 2020 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="snippy" name="snippy" version="@VERSION@+galaxy1"> +<tool id="snippy" name="snippy" version="@VERSION@+galaxy2"> <description> Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. </description> @@ -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}' ]]> </command> <inputs> |