Mercurial > repos > bgruening > deeptools_compute_gc_bias
changeset 21:d0ad59857cd1 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit cbb142cf0582948030f99621d5dd65ab80caa296
| author | bgruening |
|---|---|
| date | Thu, 11 Aug 2016 06:29:43 -0400 |
| parents | 3fee9a3af45a |
| children | 4c8645f537a3 |
| files | computeGCBias.xml deepTools_macros.xml static/images/plotEnrichment_output.png test-data/bamCompare_result1.bg test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/bamCoverage_result4.bg test-data/bamCoverage_result4.bw test-data/bamCoverage_result5.bw test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/correctGCBias_result1.bam test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt test-data/plotFingerprint_result2.tabular |
| diffstat | 16 files changed, 826 insertions(+), 727 deletions(-) [+] |
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--- a/computeGCBias.xml Fri May 13 17:21:08 2016 -0400 +++ b/computeGCBias.xml Thu Aug 11 06:29:43 2016 -0400 @@ -32,13 +32,11 @@ --sampleSize '$advancedOpt.sampleSize' --regionSize '$advancedOpt.regionSize' - #if $advancedOpt.filterOut: - --filterOut $advancedOpt.filterOut - #end if - #if $advancedOpt.extraSampling: --extraSampling $advancedOpt.extraSampling #end if + + @blacklist@ #end if #if str($image_format) != 'none': @@ -72,15 +70,10 @@ is set to 300 bases, which is close to the standard fragment size of many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read. (--regionSize)"/> - <param name="filterOut" type="data" format="bed" optional="true" - label="BED file containing genomic regions to be excluded from the estimation of the correction" - help="Such regions usually contain repetitive regions and peaks that, if included, would - bias the correction. It is recommended to filter out known repetitive regions if multi-reads - (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, - it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" /> <param name="extraSampling" type="data" format="bed" optional="true" label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome" help="(--extraSampling)" /> + <expand macro="blacklist" /> </when> </conditional> <param name="image_format" type="select"
--- a/deepTools_macros.xml Fri May 13 17:21:08 2016 -0400 +++ b/deepTools_macros.xml Thu Aug 11 06:29:43 2016 -0400 @@ -30,6 +30,25 @@ #if $advancedOpt.samFlagExclude: --samFlagExclude $advancedOpt.samFlagExclude #end if + #if $advancedOpt.minFragmentLength: + --minFragmentLength $advancedOpt.minFragmentLength + #end if + #if $advancedOpt.maxFragmentLength: + --maxFragmentLength $advancedOpt.maxFragmentLength + #end if + </token> + + <token name="@ADVANCED_OPTS_GTF@"> + $advancedOpt.metagene + #if $advancedOpt.transcriptID: + --transcriptID $advancedOpt.transcriptID + #end if + #if $advancedOpt.exonID: + --exonID $advancedOpt.exonID + #end if + #if $advancedOpt.transcript_id_designator: + --transcript_id_designator $advancedOpt.transcript_id_designator + #end if </token> <xml name="heatmap_options"> @@ -59,9 +78,9 @@ </xml> <xml name="zMin_zMax"> - <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" + <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities" help="If not specified the value is set automatically."/> - <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities" + <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities" help="If not specified the value is set automatically."/> </xml> @@ -159,14 +178,43 @@ help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/> </xml> + <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." /> + <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." /> + </xml> + <xml name="read_processing_options"> <expand macro="extendReads" /> <expand macro="ignoreDuplicates" /> <expand macro="centerReads" /> <expand macro="minMappingQuality" /> <expand macro="samFlags" /> + <expand macro="fragLength" /> </xml> + <xml name="gtf_options"> + <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue="" + label="Use a metagene model" + help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> + <param argument="--transcriptID" optional="True" value="transcript" type="text" + label="trascript designator" + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> + <param argument="--exonID" optional="True" value="exon" type="text" + label="exon designator" + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> + <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" + label="transcriptID key designator" + help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists) + or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g., + as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be + convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> + </xml> + + <xml name="plotNumbers"> <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" label="Plot the correlation value" @@ -247,7 +295,7 @@ </xml> <xml name="minMappingQuality"> - <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" + <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" label="Minimum mapping quality" help= "If set, only reads with a mapping quality score higher than this value are considered."/> </xml> @@ -363,6 +411,47 @@ ]]> </token> + <xml name="blacklist"> + <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" + label="Blacklisted regions in BED/GTF format" + help="One or more files containing regions to exclude from the analysis" /> + </xml> + + <token name="@blacklist@"> +<![CDATA[ + #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': + #set blfiles=[] + #for $f in $advancedOpt.blackListFileName: + #silent $blfiles.append("'%s'" % $f) + #end for + #if $blfiles != ["'None'"]: + --blackListFileName #echo ' '.join($blfiles)# + #end if + #end if +]]> + </token> + + <xml name="multiple_bed"> + <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" + label="Regions in BED/GTF format" + help="One or more files containing regions to include in the analysis" /> + </xml> + + <token name="@multiple_bed@"> +<![CDATA[ + #set files=[] + #set labels=[] + #for $f in $BED: + #silent $files.append("'%s'" % $f) + #silent $labels.append("'%s'" % $f.display_name) + #end for + #if len($files) > 0: + --BED #echo ' '.join($files)# + --regionLabels #echo ' '.join($labels)# + #end if +]]> + </token> + <xml name="reference_genome_source"> <conditional name="source"> <param name="ref_source" type="select" label="Reference genome"> @@ -404,7 +493,8 @@ <option value="specific">user specified</option> </param> <when value="specific"> - <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> + <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" + help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> </when> <when value="2150570000" /> <when value="2451960000" /> @@ -439,7 +529,10 @@ <when value="no" /> <when value="yes"> <yield /> - <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> + <param name="saveSortedRegions" type="boolean" + label="Save the regions after skipping zeros or min/max threshold values" + help="The order of the regions in the file follows the sorting order selected. This is useful, + for example, to generate other heatmaps keeping the sorting of the first heatmap."/> </when> </conditional> </xml> @@ -454,6 +547,11 @@ </param> </xml> + <xml name="output_dpi"> + <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" + label="Image dpi" help=""/> + </xml> + <xml name="output_image_file_format"> <data format="png" name="outFileName" label="${tool.name} image"> <change_format> @@ -497,7 +595,9 @@ </xml> <xml name="colorMap"> - <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> + <param name="colorMap" type="select" label="Color map to use for the heatmap" + help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html" + multiple="true"> <option value="RdYlBu" selected="true">RdYlBu</option> <option value="Accent">Accent</option> <option value="Spectral">Spectral</option>
--- a/test-data/bamCompare_result1.bg Fri May 13 17:21:08 2016 -0400 +++ b/test-data/bamCompare_result1.bg Thu Aug 11 06:29:43 2016 -0400 @@ -1,1 +1,1 @@ -chrM 0 16569 1.0 +chrM 0 16569 1.00
--- a/test-data/bamCoverage_result3.bg Fri May 13 17:21:08 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Thu Aug 11 06:29:43 2016 -0400 @@ -1,8 +1,7 @@ -chrM 0 10 18498299.57 -chrM 10 200 9768764.94 -chrM 200 210 10184457.07 -chrM 210 220 9976611.00 +chrM 0 210 9768764.94 +chrM 210 220 9560918.88 chrM 220 230 7690304.31 -chrM 230 240 6027535.81 +chrM 230 240 5196151.56 chrM 240 250 3325537.00 chrM 250 260 623538.19 +chrM 260 16569 0.00
--- a/test-data/bamCoverage_result4.bg Fri May 13 17:21:08 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Thu Aug 11 06:29:43 2016 -0400 @@ -1,472 +1,472 @@ -phiX174 0 10 16038.46 -phiX174 10 20 48115.38 -phiX174 20 70 144346.15 -phiX174 70 80 192461.54 -phiX174 80 90 176423.08 -phiX174 90 100 160384.62 -phiX174 100 120 112269.23 -phiX174 120 140 144346.15 -phiX174 140 150 160384.62 -phiX174 150 160 128307.69 -phiX174 160 170 160384.62 -phiX174 170 180 176423.08 -phiX174 180 200 208500.00 -phiX174 200 210 192461.54 -phiX174 210 220 240576.92 -phiX174 220 230 272653.85 -phiX174 230 240 336807.69 -phiX174 240 250 320769.23 -phiX174 250 260 288692.31 -phiX174 260 270 336807.69 -phiX174 270 280 400961.54 -phiX174 280 300 417000.00 -phiX174 300 310 352846.15 -phiX174 310 320 320769.23 -phiX174 320 330 368884.62 -phiX174 330 340 352846.15 -phiX174 340 350 288692.31 -phiX174 350 360 256615.38 -phiX174 360 370 224538.46 -phiX174 370 380 240576.92 -phiX174 380 390 304730.77 -phiX174 390 400 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--- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 17:21:08 2016 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Thu Aug 11 06:29:43 2016 -0400 @@ -1,6 +1,8 @@ + + +BAM file : 0.bam Sample size: 3 - Fragment lengths: Min.: 241.0 1st Qu.: 241.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Thu Aug 11 06:29:43 2016 -0400 @@ -0,0 +1,5 @@ +file featureType percent +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00
--- a/test-data/plotFingerprint_result2.tabular Fri May 13 17:21:08 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Thu Aug 11 06:29:43 2016 -0400 @@ -1,239 +1,239 @@ 'bowtie2 test1.bam' 'bowtie2 test1.bam' -68 68 -65 65 -61 61 -57 57 -43 43 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -29 29 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 27 27 -26 26 -22 22 +25 25 +24 24 21 21 20 20 -20 20 +19 19 +19 19 19 19 17 17 17 17