# HG changeset patch # User bgruening # Date 1517848927 18000 # Node ID 9cd1cde06157a2085aee221c08a03815727b1e0f # Parent db940c262830c58957b5f1843d136ae76cbc2356 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c diff -r db940c262830 -r 9cd1cde06157 deepTools_macros.xml --- a/deepTools_macros.xml Mon May 15 03:56:11 2017 -0400 +++ b/deepTools_macros.xml Mon Feb 05 11:42:07 2018 -0500 @@ -1,10 +1,10 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.5.1.1 + 2.5.7 - deeptools + deeptools @@ -211,7 +211,7 @@ - - - - - - - - - - - - - - - - - #if $advancedOpt.doExtendCustom.doExtend == 'custom': - --extendReads $advancedOpt.doExtendCustom.extendReadsValue - #else if $advancedOpt.doExtendCustom.doExtend == 'yes': - --extendReads - #end if - $advancedOpt.ignoreDuplicates - $advancedOpt.centerReads - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' - #end if - #if $advancedOpt.samFlagInclude: - --samFlagInclude $advancedOpt.samFlagInclude - #end if - #if $advancedOpt.samFlagExclude: - --samFlagExclude $advancedOpt.samFlagExclude - #end if - - - - - - - - - - - #if str($plotting_type.zMin) != "": - --zMin $plotting_type.zMin - #end if - #if str($plotting_type.zMax) != "": - --zMax $plotting_type.zMax - #end if - --colorMap '$plotting_type.colorMap' - $plotting_type.plotNumbers - --plotTitle '$plotting_type.plotTitle' - - - - - - - - - - - - - - - - - --numberOfProcessors "\${GALAXY_SLOTS:-4}" -<<<<<<< HEAD - 2.0.1.0 -======= - 2.1.0 ->>>>>>> d56067f86089e75354a2fad266002db3730766d9 - - - python - @BINARY@ -<<<<<<< HEAD - deepTools -======= - deepTools ->>>>>>> d56067f86089e75354a2fad266002db3730766d9 - - - - @BINARY@ --version - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': - #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': - #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: - --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans - #end if - #end if - #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': - #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: - --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust - #end if - #end if - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: infomark - -For more information on the tools, please visit our `help site`_. - -If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com - -This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. - -.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac -.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de -.. _help site: https://deeptools.readthedocs.org/ - - - - - 10.1093/nar/gku365 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #if $source.ref_source=="history": - --genome $source.input1 - #else: - --genome "$source.input1_2bit.fields.path" - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (( - output['showOutputSettings'] == 'yes' and - output['saveMatrix'] is True - )) - - - - - - - - (( - output['showOutputSettings'] == 'yes' and - output['saveSortedRegions'] is True - )) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r db940c262830 -r 9cd1cde06157 multiBigwigSummary.xml --- a/multiBigwigSummary.xml Mon May 15 03:56:11 2017 -0400 +++ b/multiBigwigSummary.xml Mon Feb 05 11:42:07 2018 -0500 @@ -18,7 +18,8 @@ @THREADS@ --outFileName $outFile - --bwfiles #echo " ".join($files)# + + --bwfiles '#echo "' '".join($files)#' --labels #echo " ".join($labels)# #if $outRawCounts: diff -r db940c262830 -r 9cd1cde06157 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Mon May 15 03:56:11 2017 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Feb 05 11:42:07 2018 -0500 @@ -1,472 +1,472 @@ -phiX174 0 10 16302.8 -phiX174 10 20 48908.5 -phiX174 20 70 146725 -phiX174 70 80 195634 -phiX174 80 90 179331 -phiX174 90 100 163028 -phiX174 100 120 114120 -phiX174 120 140 146725 -phiX174 140 150 163028 -phiX174 150 160 130423 -phiX174 160 170 163028 -phiX174 170 180 179331 -phiX174 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9cd1cde06157 test-data/bamCoverage_result5.bw Binary file test-data/bamCoverage_result5.bw has changed diff -r db940c262830 -r 9cd1cde06157 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon May 15 03:56:11 2017 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:42:07 2018 -0500 @@ -6,11 +6,11 @@ Fragment lengths: Min.: 241.0 1st Qu.: 241.5 -Mean: 244.666666667 +Mean: 244.66666666666666 Median: 242.0 3rd Qu.: 246.5 Max.: 251.0 -Std: 4.49691252108 +Std: 4.496912521077347 Read lengths: Min.: 251.0 diff -r db940c262830 -r 9cd1cde06157 test-data/heatmapper_result1.png Binary file test-data/heatmapper_result1.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotCorrelation_result1.png Binary file test-data/plotCorrelation_result1.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotCorrelation_result2.png Binary file test-data/plotCorrelation_result2.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotCoverage_result1.png Binary file test-data/plotCoverage_result1.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotEnrichment_output.txt --- a/test-data/plotEnrichment_output.txt Mon May 15 03:56:11 2017 -0400 +++ b/test-data/plotEnrichment_output.txt Mon Feb 05 11:42:07 2018 -0500 @@ -1,5 +1,5 @@ file featureType percent +bowtie2 test1.bam up 100.00 bowtie2 test1.bam down 100.00 bowtie2 test1.bam up 100.00 bowtie2 test1.bam down 100.00 -bowtie2 test1.bam up 100.00 diff -r db940c262830 -r 9cd1cde06157 test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Mon May 15 03:56:11 2017 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Feb 05 11:42:07 2018 -0500 @@ -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 0.269004498068 NA NA NA -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0 +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 NA 0.26900449806812143 NA NA NA +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.26900449806812143 0 0 0 diff -r db940c262830 -r 9cd1cde06157 test-data/plotPCA_result1.png Binary file test-data/plotPCA_result1.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotPCA_result2.png Binary file test-data/plotPCA_result2.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/plotPCA_result2.tabular --- a/test-data/plotPCA_result2.tabular Mon May 15 03:56:11 2017 -0400 +++ b/test-data/plotPCA_result2.tabular Mon Feb 05 11:42:07 2018 -0500 @@ -1,3 +1,3 @@ Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue -1 -0.707106781187 -0.707106781187 6.0 -2 -0.707106781187 0.707106781187 1.23259516441e-32 +1 -0.7071067811865476 -0.7071067811865475 6.000000000000001 +2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 diff -r db940c262830 -r 9cd1cde06157 test-data/profiler_result1.png Binary file test-data/profiler_result1.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/profiler_result2.png Binary file test-data/profiler_result2.png has changed diff -r db940c262830 -r 9cd1cde06157 test-data/profiler_result2.tabular --- a/test-data/profiler_result2.tabular Mon May 15 03:56:11 2017 -0400 +++ b/test-data/profiler_result2.tabular Mon Feb 05 11:42:07 2018 -0500 @@ -1,3 +1,3 @@ bin labels -0.0Kb 0.0Kb -bins 1 2 +bins 1.0 2.0 bamCoverage_result4_bw_0 genes 2477942.875 2610260.125