| Previous changeset 3:c1bc2d0c2e5b (2017-01-24) Next changeset 5:fa7bc5e5aea2 (2017-03-31) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289 |
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modified:
deepTools_macros.xml plotEnrichment.xml test-data/bamCompare_result2.bw test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result6.bw test-data/bamPEFragmentSize_histogram_result1.png test-data/bigwigCompare_result1.bw test-data/computeMatrixOperations.txt test-data/computeMatrixOperations_result2.mat.gz test-data/computeMatrix_result1.gz test-data/computeMatrix_result2.gz test-data/computeMatrix_result3.gz test-data/correctGCBias_result1.bam test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/multiBamSummary_result1.npz test-data/multiBamSummary_result2.npz test-data/multiBigwigSummary_result1.npz test-data/plotCorrelation_result1.png test-data/plotCorrelation_result1.tabular test-data/plotCorrelation_result2.png test-data/plotCoverage_result1.png test-data/plotEnrichment_output.png test-data/plotFingerprint_quality_metrics.tabular test-data/plotFingerprint_result1.png test-data/plotFingerprint_result2.png test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular tool_dependencies.xml |
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added:
test-data/multiBamSummary_result2b.npz |
| b |
| diff -r c1bc2d0c2e5b -r 8980933fd546 deepTools_macros.xml --- a/deepTools_macros.xml Tue Jan 24 04:55:58 2017 -0500 +++ b/deepTools_macros.xml Fri Mar 31 09:26:37 2017 -0400 |
| [ |
| @@ -1,5 +1,17 @@ <macros> + <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> + <token name="@WRAPPER_VERSION@">2.5.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement> + <yield /> + </requirements> + <expand macro="stdio" /> + <version_command>@BINARY@ --version</version_command> + </xml> + <xml name="advancedOpt_scaffold"> <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > @@ -97,18 +109,6 @@ </param> </xml> - <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.4.2</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.4.2">deeptools</requirement> - <yield /> - </requirements> - <expand macro="stdio" /> - <version_command>@BINARY@ --version</version_command> - </xml> - <xml name="smoothLength"> <param argument="--smoothLength" type="integer" value="" optional="True" min="1" label="Smooth values using the following length (in bases)" @@ -181,10 +181,10 @@ <xml name="fragLength"> <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" label="Minimum fragment length for inclusion." - help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> + help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" label="Maximum fragment length for inclusion." - help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." /> + help="A value of 0 (the default) is equivalent to no maximum." /> </xml> <xml name="read_processing_options"> @@ -324,9 +324,7 @@ <xml name="scaleFactor"> <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" - help="When used in combination with --normalizeTo1x or - --normalizeUsingRPKM, the computed scaling factor will - be multiplied by the given scale factor." /> + help="The computed scaling factor will be multiplied by this (default 1)." /> </xml> <xml name="scaleFactors"> @@ -441,19 +439,22 @@ <![CDATA[ #set files=[] #set labels=[] + #import re #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.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($bamfile.display_name)) + #silent $labels.append("'%s'" % identifier) #end for #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.metadata.bam_index}" "./${counter}.bam.bai" && #silent $files.append('%s.bam' % $counter) - #silent $labels.append("'%s'" % ($f.bamfiles.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #end if ]]> @@ -463,17 +464,20 @@ <![CDATA[ #set files=[] #set labels=[] + #import re #if $multibigwig_conditional.orderMatters == "No": #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) ln -s "${bigwig}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($bigwig.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) ln -s "${f.bigwigfiles}" "${counter}.bw" && #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name)) + #silent $labels.append("'%s'" % $identifier) #end for #end if ]]> |
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| diff -r c1bc2d0c2e5b -r 8980933fd546 plotEnrichment.xml --- a/plotEnrichment.xml Tue Jan 24 04:55:58 2017 -0500 +++ b/plotEnrichment.xml Fri Mar 31 09:26:37 2017 -0400 |
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| @@ -7,7 +7,6 @@ <expand macro="requirements" /> <command> <
