| Previous changeset 11:41b3f35b7563 (2017-01-24) Next changeset 13:c192acaeef84 (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:
bamCoverage.xml deepTools_macros.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 |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 bamCoverage.xml --- a/bamCoverage.xml Tue Jan 24 04:53:33 2017 -0500 +++ b/bamCoverage.xml Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -21,14 +21,12 @@ #if $scaling.type=='rpkm': --normalizeUsingRPKM - --scaleFactor $scaling.scaleFactor #elif $scaling.type=='1x': #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize #else: --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt #end if - --scaleFactor $scaling.scaleFactor #end if #if str($region).strip() != '': @@ -36,6 +34,10 @@ #end if #if $advancedOpt.showAdvancedOpt == "yes": + #if str($advancedOpt.scaleFactor).strip() != '': + --scaleFactor $advancedOpt.scaleFactor + #end if + #if $advancedOpt.smoothLength: --smoothLength '$advancedOpt.smoothLength' #end if @@ -74,13 +76,10 @@ <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option> <option value="no">Do not normalize or scale</option> </param> - <when value="rpkm"> - <expand macro="scaleFactor" /> - </when> + <when value="rpkm"/> <when value="no"/> <when value="1x"> <expand macro="effectiveGenomeSize" /> - <expand macro="scaleFactor" /> </when> </conditional> @@ -98,6 +97,7 @@ </param> <when value="no" /> <when value="yes"> + <expand macro="scaleFactor" /> <expand macro="smoothLength" /> <param argument="ignoreForNormalization" type="text" value="" |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 deepTools_macros.xml --- a/deepTools_macros.xml Tue Jan 24 04:53:33 2017 -0500 +++ b/deepTools_macros.xml Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -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 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCompare_result2.bw |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamCoverage_result1.bw |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/bamPEFragmentSize_histogram_result1.png |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrixOperations.txt --- a/test-data/computeMatrixOperations.txt Tue Jan 24 04:53:33 2017 -0500 +++ b/test-data/computeMatrixOperations.txt Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -1,4 +1,4 @@ Groups: genes Samples: - file_0 + bamCoverage_result4_bw_0 |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrixOperations_result2.mat.gz |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/computeMatrix_result1.gz |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/correctGCBias_result1.bam |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/multiBigwigSummary_result1.npz |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCorrelation_result1.tabular --- a/test-data/plotCorrelation_result1.tabular Tue Jan 24 04:53:33 2017 -0500 +++ b/test-data/plotCorrelation_result1.tabular Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -1,3 +1,3 @@ - 'bowtie2-test1.bam' 'bowtie2-test1.bam' -'bowtie2-test1.bam' 1.0000 1.0000 -'bowtie2-test1.bam' 1.0000 1.0000 + 'bowtie2 test1.bam' 'bowtie2 test1.bam' +'bowtie2 test1.bam' 1.0000 1.0000 +'bowtie2 test1.bam' 1.0000 1.0000 |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotCorrelation_result2.png |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotEnrichment_output.png |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Tue Jan 24 04:53:33 2017 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -1,3 +1,3 @@ Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/profiler_result1.png |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 test-data/profiler_result2.tabular --- a/test-data/profiler_result2.tabular Tue Jan 24 04:53:33 2017 -0500 +++ b/test-data/profiler_result2.tabular Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -1,3 +1,3 @@ bin labels -0.0Kb 0.0Kb bins 1 2 -file_0 genes 2477942.34473 2610259.65234 +bamCoverage_result4_bw_0 genes 2477942.875 2610260.125 |
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| diff -r 41b3f35b7563 -r 22bfbb186bf1 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 24 04:53:33 2017 -0500 +++ b/tool_dependencies.xml Fri Mar 31 08:08:52 2017 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7.10"> - <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="deeptools" version="2.4.2"> <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |
