Mercurial > repos > bgruening > deeptools_plot_coverage
changeset 37:18ef8e2c9763 draft
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
| author | bgruening |
|---|---|
| date | Fri, 11 Feb 2022 09:25:04 +0000 |
| parents | 2c17ceeae363 |
| children | 9f2108594465 |
| files | deepTools_macros.xml plotCoverage.xml repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/plotFingerprint_quality_metrics.tabular test-data/plotPCA_result2.tabular |
| diffstat | 7 files changed, 9 insertions(+), 12 deletions(-) [+] |
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--- a/deepTools_macros.xml Fri Jan 24 07:40:30 2020 +0000 +++ b/deepTools_macros.xml Fri Feb 11 09:25:04 2022 +0000 @@ -1,10 +1,10 @@ <macros> <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> - <token name="@WRAPPER_VERSION@">3.3.2.0</token> + <token name="@WRAPPER_VERSION@">3.5.1.0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="3.3.2">deeptools</requirement> + <requirement type="package" version="3.5.1">deeptools</requirement> <requirement type="package" version="1.9">samtools</requirement> </requirements> <expand macro="stdio" />
--- a/plotCoverage.xml Fri Jan 24 07:40:30 2020 +0000 +++ b/plotCoverage.xml Fri Feb 11 09:25:04 2022 +0000 @@ -26,7 +26,7 @@ #end if #if ' '.join(map(str, $BED)) != 'None': - #set bedFileLList=[] + #set bedFileList=[] #for $f in $BED: #silent $bedFileList.append("'%s'" % $f) #end for @@ -101,11 +101,8 @@ <expand macro="blacklist" /> </when> </conditional> - <expand macro="input_image_file_format" /> <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/> - - </inputs> <outputs> <expand macro="output_image_file_format_not_nested" />
--- a/repository_dependencies.xml Fri Jan 24 07:40:30 2020 +0000 +++ b/repository_dependencies.xml Fri Feb 11 09:25:04 2022 +0000 @@ -1,4 +1,4 @@ <?xml version="1.0" ?> <repositories> - <repository changeset_revision="b640d79b49cb" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/> + <repository name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="b640d79b49cb"/> </repositories> \ No newline at end of file
--- a/test-data/bamPEFragmentSize_result1.txt Fri Jan 24 07:40:30 2020 +0000 +++ b/test-data/bamPEFragmentSize_result1.txt Fri Feb 11 09:25:04 2022 +0000 @@ -12,7 +12,7 @@ Max.: 251.0 Std: 4.496912521077347 MAD: 1.0 -Len. 10%: 241.20000000000002 +Len. 10%: 241.2 Len. 20%: 241.4 Len. 30%: 241.6 Len. 40%: 241.8
--- a/test-data/bamPEFragmentSize_table1.txt Fri Jan 24 07:40:30 2020 +0000 +++ b/test-data/bamPEFragmentSize_table1.txt Fri Feb 11 09:25:04 2022 +0000 @@ -1,2 +1,2 @@ Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99% -bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.20000000000002 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 +bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.2 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0
--- a/test-data/plotFingerprint_quality_metrics.tabular Fri Jan 24 07:40:30 2020 +0000 +++ b/test-data/plotFingerprint_quality_metrics.tabular Fri Feb 11 09:25:04 2022 +0000 @@ -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 0.00493632029863651 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 +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 nan 0.2690044980681214 nan nan nan +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.2690044980681214 0 0 0
--- a/test-data/plotPCA_result2.tabular Fri Jan 24 07:40:30 2020 +0000 +++ b/test-data/plotPCA_result2.tabular Fri Feb 11 09:25:04 2022 +0000 @@ -1,4 +1,4 @@ #plotPCA --outFileNameData Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue 1 -0.7071067811865476 -0.7071067811865475 4.0 -2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 +2 -0.7071067811865475 0.7071067811865476 2.49319462166397e-32