| Previous changeset 7:65e0795278b4 (2016-05-13) Next changeset 9:e22b1110529c (2016-10-25) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe |
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modified:
bamCoverage.xml deepTools_macros.xml 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/plotFingerprint_result2.tabular tool_dependencies.xml |
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added:
static/images/plotEnrichment_output.png test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt |
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| diff -r 65e0795278b4 -r 028fcce954f1 bamCoverage.xml --- a/bamCoverage.xml Fri May 13 14:10:11 2016 -0400 +++ b/bamCoverage.xml Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -50,6 +50,12 @@ #if str($advancedOpt.filterRNAstrand) != 'no': --filterRNAstrand '$advancedOpt.filterRNAstrand' #end if + + #if $advancedOpt.Offset: + --Offset '$advancedOpt.Offset' + #end if + + @blacklist@ #end if ]]> </command> @@ -107,7 +113,19 @@ <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue="" label="Determine nucleosome positions from MNase-seq data" - help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." /> + help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data. By default, only fragments between 130 and 200 bases will be used, though this can be changed with the --minFragmentLength and --maxFragmentLength options." /> + + <param argument="--Offset" type="integer" 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. By default, the entire alignment is used to + denote where the signal is located." /> <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand." help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands. @@ -116,6 +134,7 @@ <option value="forward">forward</option> <option value="reverse">reverse</option> </param> + <expand macro="blacklist" /> </when> </conditional> |
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| diff -r 65e0795278b4 -r 028fcce954f1 deepTools_macros.xml --- a/deepTools_macros.xml Fri May 13 14:10:11 2016 -0400 +++ b/deepTools_macros.xml Mon Sep 19 18:05:26 2016 -0400 |
| [ |
| b'@@ -30,6 +30,25 @@\n #if $advancedOpt.samFlagExclude:\n --samFlagExclude $advancedOpt.samFlagExclude\n #end if\n+ #if $advancedOpt.minFragmentLength:\n+ --minFragmentLength $advancedOpt.minFragmentLength\n+ #end if\n+ #if $advancedOpt.maxFragmentLength:\n+ --maxFragmentLength $advancedOpt.maxFragmentLength\n+ #end if\n+ </token>\n+\n+ <token name="@ADVANCED_OPTS_GTF@">\n+ $advancedOpt.metagene\n+ #if $advancedOpt.transcriptID:\n+ --transcriptID $advancedOpt.transcriptID\n+ #end if\n+ #if $advancedOpt.exonID:\n+ --exonID $advancedOpt.exonID\n+ #end if\n+ #if $advancedOpt.transcript_id_designator:\n+ --transcript_id_designator $advancedOpt.transcript_id_designator\n+ #end if\n </token>\n \n <xml name="heatmap_options">\n@@ -59,9 +78,9 @@\n </xml>\n \n <xml name="zMin_zMax">\n- <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+ <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"\n help="If not specified the value is set automatically."/>\n- <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+ <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"\n help="If not specified the value is set automatically."/>\n </xml>\n \n@@ -72,18 +91,18 @@\n <sanitizer>\n <valid initial="string.letters,string.digits">\n <add value="|"/>\n+ <add value=":"/>\n </valid>\n </sanitizer>\n </param>\n </xml>\n \n <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n- <token name="@WRAPPER_VERSION@">2.2.3</token>\n+ <token name="@WRAPPER_VERSION@">2.3.5</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="2.7.10">python</requirement>\n- <requirement type="binary">@BINARY@</requirement>\n- <requirement type="package" version="2.2.3">deepTools</requirement>\n+ <requirement type="package" version="2.3.5">deepTools</requirement>\n <yield />\n </requirements>\n <expand macro="stdio" />\n@@ -159,14 +178,43 @@\n 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."/>\n </xml>\n \n+ <xml name="fragLength">\n+ <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"\n+ label="Minimum fragment length for inclusion."\n+ 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." />\n+ <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"\n+ label="Maximum fragment length for inclusion."\n+ help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />\n+ </xml>\n+\n <xml name="read_processing_options">\n <expand macro="extendReads" />\n <expand macro="ignoreDuplicates" />\n <expand macro="centerReads" />\n <expand macro="minMappingQuality" />\n <expand macro="samFlags" />\n+ <expand macro="fragLength" />\n </xml>\n \n+ <xml name="gtf_options">\n+ <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""\n+ label="Use a metagene model"\n+ 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 mRN'..b'D/GTF format"\n+ help="One or more files containing regions to exclude from the analysis" />\n+ </xml>\n+\n+ <token name="@blacklist@">\n+<![CDATA[\n+ #if \' \'.join( map(str, $advancedOpt.blackListFileName) ) != \'None\':\n+ #set blfiles=[]\n+ #for $f in $advancedOpt.blackListFileName:\n+ #silent $blfiles.append("\'%s\'" % $f)\n+ #end for\n+ #if $blfiles != ["\'None\'"]:\n+ --blackListFileName #echo \' \'.join($blfiles)#\n+ #end if\n+ #end if\n+]]> \n+ </token>\n+\n+ <xml name="multiple_bed">\n+ <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"\n+ label="Regions in BED/GTF format"\n+ help="One or more files containing regions to include in the analysis" />\n+ </xml>\n+\n+ <token name="@multiple_bed@">\n+<![CDATA[\n+ #set files=[]\n+ #set labels=[]\n+ #for $f in $BED:\n+ #silent $files.append("\'%s\'" % $f)\n+ #silent $labels.append("\'%s\'" % $f.display_name)\n+ #end for\n+ #if len($files) > 0:\n+ --BED #echo \' \'.join($files)#\n+ --regionLabels #echo \' \'.join($labels)#\n+ #end if\n+]]> \n+ </token>\n+\n <xml name="reference_genome_source">\n <conditional name="source">\n <param name="ref_source" type="select" label="Reference genome">\n@@ -404,7 +493,8 @@\n <option value="specific">user specified</option>\n </param>\n <when value="specific">\n- <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+ <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n+ help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n </when>\n <when value="2150570000" />\n <when value="2451960000" />\n@@ -439,7 +529,10 @@\n <when value="no" />\n <when value="yes">\n <yield />\n- <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."/>\n+ <param name="saveSortedRegions" type="boolean"\n+ label="Save the regions after skipping zeros or min/max threshold values"\n+ help="The order of the regions in the file follows the sorting order selected. This is useful,\n+ for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n </when>\n </conditional>\n </xml>\n@@ -454,6 +547,11 @@\n </param>\n </xml>\n \n+ <xml name="output_dpi">\n+ <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"\n+ label="Image dpi" help=""/>\n+ </xml>\n+\n <xml name="output_image_file_format">\n <data format="png" name="outFileName" label="${tool.name} image">\n <change_format>\n@@ -497,7 +595,9 @@\n </xml>\n \n <xml name="colorMap">\n- <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">\n+ <param name="colorMap" type="select" label="Color map to use for the heatmap"\n+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n+ multiple="true">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n' |
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| diff -r 65e0795278b4 -r 028fcce954f1 static/images/plotEnrichment_output.png |
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| Binary file static/images/plotEnrichment_output.png has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Fri May 13 14:10:11 2016 -0400 +++ b/test-data/bamCompare_result1.bg Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -1,1 +1,1 @@ -chrM 0 16569 1.0 +chrM 0 16569 1.00 |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCoverage_result1.bw |
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| Binary file test-data/bamCoverage_result1.bw has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Fri May 13 14:10:11 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -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 |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Fri May 13 14:10:11 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Sep 19 18:05:26 2016 -0400 |
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| b'@@ -1,472 +1,472 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|
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| Binary file test-data/bamCoverage_result5.bw has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamPEFragmentSize_histogram_result1.png |
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| Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 14:10:11 2016 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -1,6 +1,8 @@ + + +BAM file : 0.bam Sample size: 3 - Fragment lengths: Min.: 241.0 1st Qu.: 241.5 |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/plotEnrichment_output.png |
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| Binary file test-data/plotEnrichment_output.png has changed |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/plotEnrichment_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -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 |
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| diff -r 65e0795278b4 -r 028fcce954f1 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Fri May 13 14:10:11 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -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 |
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| diff -r 65e0795278b4 -r 028fcce954f1 tool_dependencies.xml --- a/tool_dependencies.xml Fri May 13 14:10:11 2016 -0400 +++ b/tool_dependencies.xml Mon Sep 19 18:05:26 2016 -0400 |
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| @@ -3,7 +3,7 @@ <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" /> </package> - <package name="deepTools" version="2.2.3"> - <repository changeset_revision="2f4601e4fc32" name="package_python_2_7_deeptools_2_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="2.3.5"> + <repository changeset_revision="c3e87c8140fe" name="package_python_2_7_deeptools_2_3_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
