Mercurial > repos > bgruening > deeptools_compute_matrix
changeset 16:8ec039dcc99a draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
| author | bgruening |
|---|---|
| date | Wed, 09 Mar 2016 17:42:04 -0500 |
| parents | e4c3016e64b4 |
| children | 66cf14fe2725 |
| files | computeMatrix.xml deepTools_macros.xml test-data/bamCoverage_result5.bw test-data/computeMatrix_result1.gz test-data/computeMatrix_result2.gz test-data/computeMatrix_result3.gz test-data/heatmapper_result1.png test-data/heatmapper_result2.png test-data/heatmapper_result2.tabular test-data/plotCorrelation_result1.png test-data/plotCoverage_result1.png test-data/plotPCA_result1.png test-data/plotPCA_result2.png test-data/plotPCA_result2.tabular test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular |
| diffstat | 17 files changed, 26 insertions(+), 8 deletions(-) [+] |
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--- a/computeMatrix.xml Thu Feb 18 11:39:00 2016 -0500 +++ b/computeMatrix.xml Wed Mar 09 17:42:04 2016 -0500 @@ -51,7 +51,12 @@ #if $mode.regionStartLength.regionStartLength_select == "yes": --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength + + --unscaled5prime $mode.regionStartLength.unscaled5prime + --unscaled3prime $mode.regionStartLength.unscaled3prime + #end if + #end if #if $advancedOpt.showAdvancedOpt == "yes": @@ -71,7 +76,6 @@ #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': --scale $advancedOpt.scale #end if - #end if ]]> </command> @@ -118,6 +122,14 @@ label="Distance downstream of the region end position" help="If the regions are genes, this would be the distance downstream of the transcription end site."/> + <param argument="--unscaled5prime" type="integer" min="0" value="0" + label="Number of bases within the gene body at the 5-prime end to exclude from scaling." + help="By default, each region is scaled to a given length (see the --regionBodyLength + option). In some cases it is useful to look at unscaled signals around region boundaries, so this + setting specifies the number of unscaled bases on the 5-prime end of each boundary." /> + <param argument="--unscaled3prime" type="integer" min="0" value="0" + label="Number of bases within the gene body at the 3-prime end to exclude from scaling." + help="As with --unscaled5prime, but for the 3-prime end." /> </when> </conditional> </when> @@ -202,9 +214,6 @@ <expand macro="output_graphic_outputs" /> <expand macro="output_save_matrix_values" /> </outputs> - <!-- - computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 - --> <tests> <test> <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
--- a/deepTools_macros.xml Thu Feb 18 11:39:00 2016 -0500 +++ b/deepTools_macros.xml Wed Mar 09 17:42:04 2016 -0500 @@ -72,12 +72,12 @@ </xml> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">2.1.0</token> + <token name="@WRAPPER_VERSION@">2.2.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2.7.10">python</requirement> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.1.0">deepTools</requirement> + <requirement type="package" version="2.2.2">deepTools</requirement> <yield /> </requirements> <expand macro="stdio" /> @@ -310,13 +310,13 @@ <xml name="multiple_input_bams"> <param argument="--bamfiles" type="data" format="bam" min="1" label="Bam file" multiple="true" - help="The BAM file must be sorted."/> + help=""/> </xml> <xml name="multiple_input_bams_min2"> <param argument="--bamfiles" type="data" format="bam" min="2" label="Bam file" multiple="true" - help="The BAM file must be sorted."/> + help=""/> </xml> <xml name="multiple_input_bigwigs">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmapper_result2.tabular Wed Mar 09 17:42:04 2016 -0500 @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234