| Previous changeset 9:9ee37f06acbc (2016-10-25) Next changeset 11:95ab4c0afab4 (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:
computeGCBias.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 9ee37f06acbc -r 4c03a58a512e computeGCBias.xml --- a/computeGCBias.xml Tue Oct 25 19:15:13 2016 -0400 +++ b/computeGCBias.xml Mon Dec 05 08:09:41 2016 -0500 |
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| @@ -111,7 +111,7 @@ <param name="input1" value="sequence.2bit" /> <param name="sampleSize" value="10" /> <param name="effectiveGenomeSize_opt" value="specific" /> - <param name="effectiveGenomeSize" value="23011544" /> + <param name="effectiveGenomeSize" value="10050" /> <param name="region" value="chr2L" /> <param name="image_format" value="none" /> <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" /> |
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| diff -r 9ee37f06acbc -r 4c03a58a512e deepTools_macros.xml --- a/deepTools_macros.xml Tue Oct 25 19:15:13 2016 -0400 +++ b/deepTools_macros.xml Mon Dec 05 08:09:41 2016 -0500 |
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| @@ -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 9ee37f06acbc -r 4c03a58a512e test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/bamCompare_result1.bg Mon Dec 05 08:09:41 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 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Mon Dec 05 08:09:41 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 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Dec 05 08:09:41 2016 -0500 |
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|
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result5.bw |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/bamCoverage_result6.bw |
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| Binary file test-data/bamCoverage_result6.bw has changed |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/bigwigCompare_result2.bg --- a/test-data/bigwigCompare_result2.bg Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/bigwigCompare_result2.bg Mon Dec 05 08:09:41 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 9ee37f06acbc -r 4c03a58a512e test-data/computeGCBias_result1.tabular --- a/test-data/computeGCBias_result1.tabular Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/computeGCBias_result1.tabular Mon Dec 05 08:09:41 2016 -0500 |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/computeMatrixOperations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrixOperations.txt Mon Dec 05 08:09:41 2016 -0500 |
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| @@ -0,0 +1,4 @@ +Groups: + genes +Samples: + file_0 |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/computeMatrixOperations_result2.mat.gz |
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| diff -r 9ee37f06acbc -r 4c03a58a512e test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r 9ee37f06acbc -r 4c03a58a512e 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 08:09:41 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 9ee37f06acbc -r 4c03a58a512e test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Tue Oct 25 19:15:13 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Mon Dec 05 08:09:41 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 9ee37f06acbc -r 4c03a58a512e test-data/sequence.2bit |
| b |
| Binary file test-data/sequence.2bit has changed |
| b |
| diff -r 9ee37f06acbc -r 4c03a58a512e tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 25 19:15:13 2016 -0400 +++ b/tool_dependencies.xml Mon Dec 05 08:09:41 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> |