Mercurial > repos > bgruening > deeptools_correct_gc_bias
changeset 19:9e60bf557373 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
| author | bgruening |
|---|---|
| date | Thu, 05 Apr 2018 10:55:12 -0400 |
| parents | cef5cec10544 |
| children | 0f86f4c83e2c |
| files | correctGCBias.xml deepTools_macros.xml test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz |
| diffstat | 4 files changed, 10 insertions(+), 9 deletions(-) [+] |
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--- a/correctGCBias.xml Fri Mar 02 16:03:21 2018 -0500 +++ b/correctGCBias.xml Thu Apr 05 10:55:12 2018 -0400 @@ -7,7 +7,7 @@ <expand macro="requirements" /> <command> <![CDATA[ - ln -s "$bamInput" "local_bamInput.bam" && + ln -s '$bamInput' local_bamInput.bam && #if $bamInput.ext == 'bam': ln -s '${bamInput.metadata.bam_index}' local_bamInput.bam.bai && #else: @@ -17,7 +17,7 @@ @BINARY@ @THREADS@ --bamfile local_bamInput.bam - --GCbiasFrequenciesFile "$GCbiasFrequenciesFile" + --GCbiasFrequenciesFile '$GCbiasFrequenciesFile' @reference_genome_source@
--- a/deepTools_macros.xml Fri Mar 02 16:03:21 2018 -0500 +++ b/deepTools_macros.xml Thu Apr 05 10:55:12 2018 -0400 @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.0.1</token> + <token name="@WRAPPER_VERSION@">3.0.2</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.0.1">deeptools</requirement> + <requirement type="package" version="3.0.2">deeptools</requirement> <requirement type="package" version="1.7">samtools</requirement> </requirements> <expand macro="stdio" /> @@ -118,6 +118,7 @@ <valid initial="string.letters,string.digits"> <add value="|"/> <add value=":"/> + <add value="."/> </valid> </sanitizer> </param> @@ -443,7 +444,7 @@ #if $multibam_conditional.orderMatters == "No": #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) - ln -s "${bamfile}" "./${counter}.bam" && + ln -s '${bamfile}' './${counter}.bam' && #if $bamfile.ext == 'bam': ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && #else: @@ -455,7 +456,7 @@ #else: #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) - ln -s "${f.bamfiles}" "./${counter}.bam" && + ln -s '${f.bamfiles}' './${counter}.bam' && #if $f.bamfiles.ext == 'bam': ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && #else: @@ -476,14 +477,14 @@ #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) - ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && + ln -f -s '${bigwig}' '${identifier}_${counter}.bw' && #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) - ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && + ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' && #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) #silent $labels.append("'%s'" % $identifier) #end for @@ -556,7 +557,7 @@ #if $source.ref_source=="history": --genome $source.input1 #else: - --genome "$source.input1_2bit.fields.path" + --genome '$source.input1_2bit.fields.path' #end if </token>