| Previous changeset 9:e22b1110529c (2016-10-25) Next changeset 11:41b3f35b7563 (2017-01-24) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09 |
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modified:
bamCoverage.xml deepTools_macros.xml test-data/bamCompare_result1.bg 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/bigwigCompare_result2.bg test-data/computeGCBias_result1.tabular test-data/correctGCBias_result1.bam test-data/plotFingerprint_result2.tabular test-data/sequence.2bit tool_dependencies.xml |
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added:
test-data/bamCoverage_result6.bw test-data/computeMatrixOperations.txt test-data/computeMatrixOperations_result2.mat.gz test-data/plotFingerprint_quality_metrics.tabular |
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| diff -r e22b1110529c -r aa33302db115 bamCoverage.xml --- a/bamCoverage.xml Tue Oct 25 19:12:11 2016 -0400 +++ b/bamCoverage.xml Mon Dec 05 08:08:15 2016 -0500 |
| [ |
| @@ -52,7 +52,7 @@ #end if #if $advancedOpt.Offset: - --Offset '$advancedOpt.Offset' + --Offset $advancedOpt.Offset #end if @blacklist@ @@ -115,7 +115,7 @@ 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. 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" + <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 @@ -124,8 +124,10 @@ 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." /> + 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." /> <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. @@ -192,6 +194,17 @@ <param name="binSize" value="10" /> <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" /> </test> + <test> + <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="binSize" value="10" /> + <param name="Offset" value="-4 -1" /> + <param name="doExtend" value="yes" /> + <param name="minMappingQuality" value="0" /> + <param name="type" value="no" /> + <output name="outFileName" file="bamCoverage_result6.bw" ftype="bigwig" /> + </test> </tests> <help> <![CDATA[ |
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| diff -r e22b1110529c -r aa33302db115 deepTools_macros.xml --- a/deepTools_macros.xml Tue Oct 25 19:12:11 2016 -0400 +++ b/deepTools_macros.xml Mon Dec 05 08:08:15 2016 -0500 |
| [ |
| @@ -98,11 +98,11 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.3.6</token> + <token name="@WRAPPER_VERSION@">2.4.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> - <requirement type="package" version="2.3.6">deepTools</requirement> + <requirement type="package" version="2.4.1">deeptools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -285,11 +285,21 @@ </param> </xml> + <xml name="sortRegionsComputeMatrix"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="keep" selected="true">maintain the same ordering as the input files</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + <xml name="sortRegions"> <param argument="--sortRegions" type="select" label="Sort regions" help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> <option value="no">no ordering</option> - <option value="descend" selected="true">descending order</option> + <option value="descend">descending order</option> <option value="ascend">ascending order</option> </param> </xml> @@ -362,21 +372,62 @@ </xml> <xml name="multiple_input_bams"> - <param argument="--bamfiles" type="data" format="bam" min="1" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="1" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bams_min2"> - <param argument="--bamfiles" type="data" format="bam" min="2" - label="Bam file" multiple="true" - help=""/> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="2" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="2" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> </xml> <xml name="multiple_input_bigwigs"> - <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" - label="Bigwig file" - help="A Bigwig file."/> + <conditional name="multibigwig_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" + label="Bigwig file" + help="A Bigwig file."/> + </when> + <when value="Yes"> + <repeat name="multibigwig_repeats" min="2" title="BigWig files"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> + </repeat> + </when> + </conditional> </xml> <xml name="plotTitle"> @@ -390,12 +441,21 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bamfile in enumerate($bamfiles): - 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)) - #end for + #if $multibam_conditional.orderMatters == "No": + #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): + 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)) + #end for + #else: + #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): + ln -s "${f.bamfile}" "./${counter}.bam" && + ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($f.bamfile.display_name)) + #end for + #end if ]]> </token> @@ -403,11 +463,19 @@ <![CDATA[ #set files=[] #set labels=[] - #for $counter, $bigwig in enumerate($bigwigfiles): - ln -s "${bigwig}" "${counter}.bw" && - #silent $files.append('%s.bw' % $counter) - #silent $labels.append("'%s'" % ($bigwig.display_name)) - #end for + #if $multibigwig_conditional.orderMatters == "No": + #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + ln -s "${bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($bigwig.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + ln -s "${f.bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($f.bigwig.display_name)) + #end for + #end if ]]> </token> |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/bamCompare_result1.bg Mon Dec 05 08:08:15 2016 -0500 |
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| @@ -1,1 +1,1 @@ -chrM 0 16569 1.00 +chrM 0 16569 1 |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Mon Dec 05 08:08:15 2016 -0500 |
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| @@ -1,7 +1,7 @@ -chrM 0 210 9768764.94 -chrM 210 220 9560918.88 -chrM 220 230 7690304.31 -chrM 230 240 5196151.56 -chrM 240 250 3325537.00 -chrM 250 260 623538.19 -chrM 260 16569 0.00 +chrM 0 210 9.76876e+06 +chrM 210 220 9.56092e+06 +chrM 220 230 7.6903e+06 +chrM 230 240 5.19615e+06 +chrM 240 250 3.32554e+06 +chrM 250 260 623538 +chrM 260 16569 0 |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Dec 05 08:08:15 2016 -0500 |
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| b'@@ -1,472 +1,472 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|
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result5.bw |
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| Binary file test-data/bamCoverage_result5.bw has changed |
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| diff -r e22b1110529c -r aa33302db115 test-data/bamCoverage_result6.bw |
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| Binary file test-data/bamCoverage_result6.bw has changed |
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| diff -r e22b1110529c -r aa33302db115 test-data/bigwigCompare_result2.bg --- a/test-data/bigwigCompare_result2.bg Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/bigwigCompare_result2.bg Mon Dec 05 08:08:15 2016 -0500 |
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| @@ -1,3 +1,3 @@ -ch1 0 400 1.0 -ch2 0 400 1.0 -ch3 0 400 1.0 +ch1 0 400 1 +ch2 0 400 1 +ch3 0 400 1 |
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| diff -r e22b1110529c -r aa33302db115 test-data/computeGCBias_result1.tabular --- a/test-data/computeGCBias_result1.tabular Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/computeGCBias_result1.tabular Mon Dec 05 08:08:15 2016 -0500 |
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| diff -r e22b1110529c -r aa33302db115 test-data/computeMatrixOperations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrixOperations.txt Mon Dec 05 08:08:15 2016 -0500 |
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| @@ -0,0 +1,4 @@ +Groups: + genes +Samples: + file_0 |
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| diff -r e22b1110529c -r aa33302db115 test-data/computeMatrixOperations_result2.mat.gz |
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| diff -r e22b1110529c -r aa33302db115 test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r e22b1110529c -r aa33302db115 test-data/plotFingerprint_quality_metrics.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Dec 05 08:08:15 2016 -0500 |
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| @@ -0,0 +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 |
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| diff -r e22b1110529c -r aa33302db115 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Tue Oct 25 19:12:11 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Mon Dec 05 08:08:15 2016 -0500 |
| b |
| @@ -1,254 +1,254 @@ 'bowtie2 test1.bam' 'bowtie2 test1.bam' -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -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 -25 25 +1085 1085 +1782 1782 +2706 2706 +3570 3570 +6753 6753 +8069 8069 +8034 8034 +7999 7999 +7964 7964 +7929 7929 +7894 7894 +7859 7859 +7824 7824 +7789 7789 +7754 7754 +7719 7719 +7684 7684 +7649 7649 +7614 7614 +7579 7579 +7544 7544 +7509 7509 +7474 7474 +7439 7439 +7404 7404 +7369 7369 +7334 7334 +7299 7299 +7264 7264 +7229 7229 +7194 7194 +7159 7159 +7124 7124 +7089 7089 +7054 7054 +7019 7019 +6984 6984 +6949 6949 +6914 6914 +6879 6879 +6844 6844 +6809 6809 +6774 6774 +6739 6739 +6704 6704 +6669 6669 +6634 6634 +6599 6599 +6564 6564 +6529 6529 +6494 6494 +6459 6459 +6424 6424 +6389 6389 +6354 6354 +6319 6319 +6284 6284 +6249 6249 +6214 6214 +6179 6179 +6144 6144 +6109 6109 +6074 6074 +6039 6039 +6004 6004 +5969 5969 +5934 5934 +5899 5899 +5864 5864 +5829 5829 +5794 5794 +5759 5759 +5724 5724 +5689 5689 +5654 5654 +5619 5619 +5584 5584 +5549 5549 +5514 5514 +5479 5479 +5444 5444 +5409 5409 +5374 5374 +5339 5339 +5304 5304 +5269 5269 +5234 5234 +5199 5199 +5164 5164 +5129 5129 +5094 5094 +5059 5059 +5024 5024 +4989 4989 +4954 4954 +4919 4919 +4884 4884 +4849 4849 +4814 4814 +4779 4779 +4744 4744 +4709 4709 +4674 4674 +4639 4639 +4604 4604 +4569 4569 +4534 4534 +4499 4499 +4464 4464 +4429 4429 +4394 4394 +4359 4359 +4324 4324 +4289 4289 +4254 4254 +4219 4219 +4184 4184 +4149 4149 +4114 4114 +4079 4079 +4044 4044 +4009 4009 +3974 3974 +3939 3939 +3904 3904 +3869 3869 +3834 3834 +3799 3799 +3764 3764 +3729 3729 +3694 3694 +3659 3659 +3624 3624 +3589 3589 +3554 3554 +3519 3519 +3484 3484 +3449 3449 +3414 3414 +3379 3379 +3344 3344 +3309 3309 +3274 3274 +3239 3239 +3204 3204 +3169 3169 +3134 3134 +3099 3099 +3064 3064 +3029 3029 +2994 2994 +2959 2959 +2924 2924 +2889 2889 +2854 2854 +2819 2819 +2784 2784 +2749 2749 +2714 2714 +2679 2679 +2644 2644 +2609 2609 +2574 2574 +2539 2539 +2504 2504 +2469 2469 +2434 2434 +2399 2399 +2364 2364 +2329 2329 +2294 2294 +2259 2259 +2224 2224 +2189 2189 +2154 2154 +2119 2119 +2084 2084 +2049 2049 +2014 2014 +1979 1979 +1944 1944 +1909 1909 +1874 1874 +1839 1839 +1804 1804 +1769 1769 +1734 1734 +1699 1699 +1664 1664 +1629 1629 +1594 1594 +1559 1559 +1524 1524 +1489 1489 +1454 1454 +1419 1419 +1384 1384 +1349 1349 +1314 1314 +1279 1279 +1244 1244 +1209 1209 +1174 1174 +1139 1139 +1104 1104 +1069 1069 +1034 1034 +999 999 +964 964 +929 929 +894 894 +859 859 +824 824 +789 789 +754 754 +719 719 +684 684 +651 651 +618 618 +585 585 +552 552 +519 519 +486 486 +453 453 +420 420 +387 387 +354 354 +321 321 +288 288 +261 261 +236 236 +227 227 +206 206 +186 186 +167 167 +160 160 +141 141 +124 124 +107 107 +92 92 +77 77 +62 62 +52 52 +45 45 +38 38 +31 31 24 24 -21 21 -20 20 -19 19 -19 19 -19 19 -17 17 -17 17 -15 15 -15 15 -15 15 -10 10 -7 7 -7 7 -7 7 -7 7 -6 6 -5 5 -5 5 -5 5 +18 18 +13 13 +8 8 3 3 0 0 0 0 |
| b |
| diff -r e22b1110529c -r aa33302db115 test-data/sequence.2bit |
| b |
| Binary file test-data/sequence.2bit has changed |
| b |
| diff -r e22b1110529c -r aa33302db115 tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 25 19:12:11 2016 -0400 +++ b/tool_dependencies.xml Mon Dec 05 08:08:15 2016 -0500 |
| b |
| @@ -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="2.3.6"> - <repository changeset_revision="05f46fef1ea5" name="package_python_2_7_deeptools_2_3_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deeptools" version="2.4.1"> + <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |