Mercurial > repos > bgruening > deeptools_plot_profile
changeset 3:c73c5d2c94b3 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
| author | bgruening |
|---|---|
| date | Wed, 09 Mar 2016 18:36:45 -0500 |
| parents | 0b9bc8b4d0c1 |
| children | 1dd2fed2ed5c |
| files | deepTools_macros.xml plotProfiler.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(+), 4 deletions(-) [+] |
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--- a/deepTools_macros.xml Thu Feb 18 11:54:57 2016 -0500 +++ b/deepTools_macros.xml Wed Mar 09 18:36:45 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">
--- a/plotProfiler.xml Thu Feb 18 11:54:57 2016 -0500 +++ b/plotProfiler.xml Wed Mar 09 18:36:45 2016 -0500 @@ -60,6 +60,10 @@ --yMax $advancedOpt.yMax #end if + #if $advancedOpt.outFileNameData: + --outFileNameData "$output_outFileNameData" + #end if + @KMEANS_CLUSTERING@ #end if @@ -154,6 +158,8 @@ label="Make one plot per group of regions" help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " /> + <param argument="--outFileNameData" type="boolean" label="Save the data underlying the average profile" + help="This option will create an additional output file." /> <param argument="--yMin" type="float" value="" size="3" optional="true" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> @@ -168,6 +174,11 @@ <outputs> <expand macro="output_image_file_format" /> <expand macro="output_graphic_outputs" /> + + <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: Underlying data"> + <filter>outFileNameData</filter> + </data> + </outputs> <tests> <test> @@ -178,7 +189,9 @@ <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> <param name="showAdvancedOpt" value="yes" /> <param name="showScaleRegionsOpt" value="yes" /> + <param name="outFileNameData" value="True" /> <output name="outFileName" file="profiler_result2.png" ftype="png" compare="sim_size" delta="4000" /> + <output name="output_outFileNameData" file="profiler_result2.tabular" ftype="tabular" /> </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmapper_result2.tabular Wed Mar 09 18:36:45 2016 -0500 @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234