Mercurial > repos > bgruening > deeptools_plot_enrichment
changeset 4:8980933fd546 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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--- 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 ]]>
--- a/plotEnrichment.xml Tue Jan 24 04:55:58 2017 -0500 +++ b/plotEnrichment.xml Fri Mar 31 09:26:37 2017 -0400 @@ -7,7 +7,6 @@ <expand macro="requirements" /> <command> <![CDATA[ - @multiple_input_bams@ @BINARY@ @THREADS@ @@ -64,6 +63,10 @@ @ADVANCED_OPTS_READ_PROCESSING@ + #if $advancedOpt.Offset: + --Offset $advancedOpt.Offset + #end if + @blacklist@ $advancedOpt.keepExons @@ -134,6 +137,20 @@ label="Include BED12 exons" help="Only for BED12 files, include columns 10-12 rather than just 2 and 3." /> + <param argument="--Offset" type="text" value="" optional="True" + label="Offset inside each alignment to use for the signal location." + help="Uses this offset inside of each read as the signal. This is useful in + cases like RiboSeq or GROseq, where only the 12th, 15th or 1st base aligned + should be used to denote where the signal is (rather than the span of the + whole alignment). This can be paired with the --filterRNAstrand option. Note + that negative values indicate offsets from the end of each read. A value of + 1 indicates the first base of the alignment (taking alignment orientation + into account). Likewise, a value of -1 is the last base of the alignment. An + offset of 0 is not permitted. If two values (separated by spaces) are specified, then they will be + used to specify a range of positions. Note that specifying something like + --Offset 5 -1 will result in the 5th through last position being used, which + is equivalent to trimming 4 bases from the 5-prime end of alignments." /> + <expand macro="blacklist" /> </expand>
--- a/test-data/computeMatrixOperations.txt Tue Jan 24 04:55:58 2017 -0500 +++ b/test-data/computeMatrixOperations.txt Fri Mar 31 09:26:37 2017 -0400 @@ -1,4 +1,4 @@ Groups: genes Samples: - file_0 + bamCoverage_result4_bw_0
--- a/test-data/plotCorrelation_result1.tabular Tue Jan 24 04:55:58 2017 -0500 +++ b/test-data/plotCorrelation_result1.tabular Fri Mar 31 09:26:37 2017 -0400 @@ -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
--- a/test-data/plotFingerprint_quality_metrics.tabular Tue Jan 24 04:55:58 2017 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Mar 31 09:26:37 2017 -0400 @@ -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
--- a/test-data/profiler_result2.tabular Tue Jan 24 04:55:58 2017 -0500 +++ b/test-data/profiler_result2.tabular Fri Mar 31 09:26:37 2017 -0400 @@ -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
--- a/tool_dependencies.xml Tue Jan 24 04:55:58 2017 -0500 +++ b/tool_dependencies.xml Fri Mar 31 09:26:37 2017 -0400 @@ -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" />