Mercurial > repos > bgruening > deeptools_plot_coverage
changeset 28:9368fbc49c8b draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
| author | bgruening |
|---|---|
| date | Thu, 01 Jun 2023 14:39:07 +0000 |
| parents | 7fda5607e777 |
| children | 231994413f89 |
| files | deepTools_macros.xml plotCoverage.xml test-data/bigwigAverage2.bw test-data/multiBigwigSummary_result1.npz test-data/multiBigwigSummary_result2.npz test-data/multiBigwigSummary_result2.tabular test-data/test_compated.bw test-data/test_half.bw |
| diffstat | 8 files changed, 249 insertions(+), 7 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Feb 11 15:16:22 2022 +0000 +++ b/deepTools_macros.xml Thu Jun 01 14:39:07 2023 +0000 @@ -1,10 +1,11 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.5.1.0</token> + <token name="@TOOL_VERSION@">3.5.2</token> + <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.5.1">deeptools</requirement> + <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" /> @@ -368,7 +369,6 @@ <xml name="pseudocount"> <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> </xml> - <token name="@REFERENCES@"> .. class:: infomark @@ -483,7 +483,7 @@ <token name="@multiple_input_bams@"> <![CDATA[ #if $custom_sample_labels_conditional.custom_labels_select == "Yes": - #set custom_labels=labels + #set custom_labels=$custom_sample_labels_conditional.labels #end if #set files=[] #set labels=[] @@ -498,7 +498,7 @@ ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && #end if #silent $files.append("'%s.bam'" % $counter) - #silent $labels.append("'%s'" % identifier) + #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): @@ -522,7 +522,7 @@ <token name="@multiple_input_bigwigs@"> <![CDATA[ #if $custom_sample_labels_conditional.custom_labels_select == "Yes": - #set custom_labels=labels + #set custom_labels=$custom_sample_labels_conditional.labels #end if #set files=[] #set labels=[]
--- a/plotCoverage.xml Fri Feb 11 15:16:22 2022 +0000 +++ b/plotCoverage.xml Thu Jun 01 14:39:07 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0" profile="18.01"> +<tool id="deeptools_plot_coverage" name="plotCoverage" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@"> <description>assesses the sequencing depth of BAM/CRAM files </description> <macros> <token name="@BINARY@">plotCoverage</token>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBigwigSummary_result2.npz Thu Jun 01 14:39:07 2023 +0000 @@ -0,0 +1,121 @@ +#'chr' 'start' 'end' 'sample1' 'sample2' +ch1 0 10 0.0 0.0 +ch1 10 20 0.0 0.0 +ch1 20 30 0.0 0.0 +ch1 30 40 0.0 0.0 +ch1 40 50 0.0 0.0 +ch1 50 60 0.0 0.0 +ch1 60 70 0.0 0.0 +ch1 70 80 0.0 0.0 +ch1 80 90 0.0 0.0 +ch1 90 100 0.0 0.0 +ch1 100 110 2.0 2.0 +ch1 110 120 2.0 2.0 +ch1 120 130 1.0 1.0 +ch1 130 140 0.0 0.0 +ch1 140 150 0.0 0.0 +ch1 150 160 0.0 0.0 +ch1 160 170 0.0 0.0 +ch1 170 180 0.0 0.0 +ch1 180 190 0.0 0.0 +ch1 190 200 0.0 0.0 +ch1 200 210 0.0 0.0 +ch1 210 220 0.0 0.0 +ch1 220 230 0.0 0.0 +ch1 230 240 0.0 0.0 +ch1 240 250 0.0 0.0 +ch1 250 260 0.0 0.0 +ch1 260 270 0.0 0.0 +ch1 270 280 0.0 0.0 +ch1 280 290 0.0 0.0 +ch1 290 300 0.0 0.0 +ch1 300 310 0.0 0.0 +ch1 310 320 0.0 0.0 +ch1 320 330 0.0 0.0 +ch1 330 340 0.0 0.0 +ch1 340 350 0.0 0.0 +ch1 350 360 0.0 0.0 +ch1 360 370 0.0 0.0 +ch1 370 380 0.0 0.0 +ch1 380 390 0.0 0.0 +ch1 390 400 0.0 0.0 +ch2 0 10 0.0 0.0 +ch2 10 20 0.0 0.0 +ch2 20 30 0.0 0.0 +ch2 30 40 0.0 0.0 +ch2 40 50 0.0 0.0 +ch2 50 60 3.0 3.0 +ch2 60 70 3.0 3.0 +ch2 70 80 1.5 1.5 +ch2 80 90 0.0 0.0 +ch2 90 100 0.0 0.0 +ch2 100 110 0.0 0.0 +ch2 110 120 0.0 0.0 +ch2 120 130 0.0 0.0 +ch2 130 140 0.0 0.0 +ch2 140 150 0.0 0.0 +ch2 150 160 1.0 1.0 +ch2 160 170 1.0 1.0 +ch2 170 180 0.5 0.5 +ch2 180 190 0.0 0.0 +ch2 190 200 0.0 0.0 +ch2 200 210 0.0 0.0 +ch2 210 220 0.0 0.0 +ch2 220 230 0.0 0.0 +ch2 230 240 0.0 0.0 +ch2 240 250 0.0 0.0 +ch2 250 260 0.0 0.0 +ch2 260 270 0.0 0.0 +ch2 270 280 0.0 0.0 +ch2 280 290 0.0 0.0 +ch2 290 300 0.0 0.0 +ch2 300 310 0.0 0.0 +ch2 310 320 0.0 0.0 +ch2 320 330 0.0 0.0 +ch2 330 340 0.0 0.0 +ch2 340 350 0.0 0.0 +ch2 350 360 0.0 0.0 +ch2 360 370 0.0 0.0 +ch2 370 380 0.0 0.0 +ch2 380 390 0.0 0.0 +ch2 390 400 0.0 0.0 +ch3 0 10 0.0 0.0 +ch3 10 20 0.0 0.0 +ch3 20 30 0.0 0.0 +ch3 30 40 0.0 0.0 +ch3 40 50 0.0 0.0 +ch3 50 60 3.0 3.0 +ch3 60 70 3.0 3.0 +ch3 70 80 1.5 1.5 +ch3 80 90 0.0 0.0 +ch3 90 100 0.0 0.0 +ch3 100 110 0.0 0.0 +ch3 110 120 0.0 0.0 +ch3 120 130 0.0 0.0 +ch3 130 140 0.0 0.0 +ch3 140 150 0.0 0.0 +ch3 150 160 1.0 1.0 +ch3 160 170 1.0 1.0 +ch3 170 180 0.5 0.5 +ch3 180 190 0.0 0.0 +ch3 190 200 0.0 0.0 +ch3 200 210 0.0 0.0 +ch3 210 220 0.0 0.0 +ch3 220 230 0.0 0.0 +ch3 230 240 0.0 0.0 +ch3 240 250 0.0 0.0 +ch3 250 260 0.0 0.0 +ch3 260 270 0.0 0.0 +ch3 270 280 0.0 0.0 +ch3 280 290 0.0 0.0 +ch3 290 300 0.0 0.0 +ch3 300 310 0.0 0.0 +ch3 310 320 0.0 0.0 +ch3 320 330 0.0 0.0 +ch3 330 340 0.0 0.0 +ch3 340 350 0.0 0.0 +ch3 350 360 0.0 0.0 +ch3 360 370 0.0 0.0 +ch3 370 380 0.0 0.0 +ch3 380 390 0.0 0.0 +ch3 390 400 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBigwigSummary_result2.tabular Thu Jun 01 14:39:07 2023 +0000 @@ -0,0 +1,121 @@ +#'chr' 'start' 'end' 'sample1' 'sample2' +ch1 0 10 0.0 0.0 +ch1 10 20 0.0 0.0 +ch1 20 30 0.0 0.0 +ch1 30 40 0.0 0.0 +ch1 40 50 0.0 0.0 +ch1 50 60 0.0 0.0 +ch1 60 70 0.0 0.0 +ch1 70 80 0.0 0.0 +ch1 80 90 0.0 0.0 +ch1 90 100 0.0 0.0 +ch1 100 110 2.0 2.0 +ch1 110 120 2.0 2.0 +ch1 120 130 1.0 1.0 +ch1 130 140 0.0 0.0 +ch1 140 150 0.0 0.0 +ch1 150 160 0.0 0.0 +ch1 160 170 0.0 0.0 +ch1 170 180 0.0 0.0 +ch1 180 190 0.0 0.0 +ch1 190 200 0.0 0.0 +ch1 200 210 0.0 0.0 +ch1 210 220 0.0 0.0 +ch1 220 230 0.0 0.0 +ch1 230 240 0.0 0.0 +ch1 240 250 0.0 0.0 +ch1 250 260 0.0 0.0 +ch1 260 270 0.0 0.0 +ch1 270 280 0.0 0.0 +ch1 280 290 0.0 0.0 +ch1 290 300 0.0 0.0 +ch1 300 310 0.0 0.0 +ch1 310 320 0.0 0.0 +ch1 320 330 0.0 0.0 +ch1 330 340 0.0 0.0 +ch1 340 350 0.0 0.0 +ch1 350 360 0.0 0.0 +ch1 360 370 0.0 0.0 +ch1 370 380 0.0 0.0 +ch1 380 390 0.0 0.0 +ch1 390 400 0.0 0.0 +ch2 0 10 0.0 0.0 +ch2 10 20 0.0 0.0 +ch2 20 30 0.0 0.0 +ch2 30 40 0.0 0.0 +ch2 40 50 0.0 0.0 +ch2 50 60 3.0 3.0 +ch2 60 70 3.0 3.0 +ch2 70 80 1.5 1.5 +ch2 80 90 0.0 0.0 +ch2 90 100 0.0 0.0 +ch2 100 110 0.0 0.0 +ch2 110 120 0.0 0.0 +ch2 120 130 0.0 0.0 +ch2 130 140 0.0 0.0 +ch2 140 150 0.0 0.0 +ch2 150 160 1.0 1.0 +ch2 160 170 1.0 1.0 +ch2 170 180 0.5 0.5 +ch2 180 190 0.0 0.0 +ch2 190 200 0.0 0.0 +ch2 200 210 0.0 0.0 +ch2 210 220 0.0 0.0 +ch2 220 230 0.0 0.0 +ch2 230 240 0.0 0.0 +ch2 240 250 0.0 0.0 +ch2 250 260 0.0 0.0 +ch2 260 270 0.0 0.0 +ch2 270 280 0.0 0.0 +ch2 280 290 0.0 0.0 +ch2 290 300 0.0 0.0 +ch2 300 310 0.0 0.0 +ch2 310 320 0.0 0.0 +ch2 320 330 0.0 0.0 +ch2 330 340 0.0 0.0 +ch2 340 350 0.0 0.0 +ch2 350 360 0.0 0.0 +ch2 360 370 0.0 0.0 +ch2 370 380 0.0 0.0 +ch2 380 390 0.0 0.0 +ch2 390 400 0.0 0.0 +ch3 0 10 0.0 0.0 +ch3 10 20 0.0 0.0 +ch3 20 30 0.0 0.0 +ch3 30 40 0.0 0.0 +ch3 40 50 0.0 0.0 +ch3 50 60 3.0 3.0 +ch3 60 70 3.0 3.0 +ch3 70 80 1.5 1.5 +ch3 80 90 0.0 0.0 +ch3 90 100 0.0 0.0 +ch3 100 110 0.0 0.0 +ch3 110 120 0.0 0.0 +ch3 120 130 0.0 0.0 +ch3 130 140 0.0 0.0 +ch3 140 150 0.0 0.0 +ch3 150 160 1.0 1.0 +ch3 160 170 1.0 1.0 +ch3 170 180 0.5 0.5 +ch3 180 190 0.0 0.0 +ch3 190 200 0.0 0.0 +ch3 200 210 0.0 0.0 +ch3 210 220 0.0 0.0 +ch3 220 230 0.0 0.0 +ch3 230 240 0.0 0.0 +ch3 240 250 0.0 0.0 +ch3 250 260 0.0 0.0 +ch3 260 270 0.0 0.0 +ch3 270 280 0.0 0.0 +ch3 280 290 0.0 0.0 +ch3 290 300 0.0 0.0 +ch3 300 310 0.0 0.0 +ch3 310 320 0.0 0.0 +ch3 320 330 0.0 0.0 +ch3 330 340 0.0 0.0 +ch3 340 350 0.0 0.0 +ch3 350 360 0.0 0.0 +ch3 360 370 0.0 0.0 +ch3 370 380 0.0 0.0 +ch3 380 390 0.0 0.0 +ch3 390 400 0.0 0.0