Mercurial > repos > bgruening > deeptools_estimatereadfiltering
changeset 10:bd1f40ce9769 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
| author | bgruening |
|---|---|
| date | Thu, 18 May 2023 20:45:20 +0000 |
| parents | 71082dac170c |
| children | bddbd9538b08 |
| files | deepTools_macros.xml readme.rst repository_dependencies.xml test-data/bamPEFragmentSize_result1.txt test-data/bamPEFragmentSize_table1.txt test-data/bigwigAverage2.bw test-data/multiBigwigSummary_result1.npz test-data/multiBigwigSummary_result2.npz test-data/multiBigwigSummary_result2.tabular test-data/plotFingerprint_quality_metrics.tabular test-data/plotPCA_result2.tabular test-data/test_compated.bw test-data/test_half.bw |
| diffstat | 13 files changed, 252 insertions(+), 89 deletions(-) [+] |
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--- a/deepTools_macros.xml Sat Jan 25 05:11:38 2020 -0500 +++ b/deepTools_macros.xml Thu May 18 20:45:20 2023 +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" /> @@ -368,7 +368,6 @@ <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 +482,7 @@ <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 +497,7 @@ 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 +521,7 @@ <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/readme.rst Sat Jan 25 05:11:38 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -======================== -Galaxy deeptools wrapper -======================== - -deepTools are user-friendly tools for the normalization and visualization of -deep-sequencing data. -They address the challenge of visualizing the large amounts of data that are now -routinely generated from sequencing centers in a meaningful way. -To do so, deepTools contain useful routines to process the mapped reads data -through removal of duplicates and different filtering options to create coverage -files in standard bedGraph and bigWig file formats. deepTools allow the creation -of normalized coverage files or the comparison between two files -(for example, treatment and control). Finally, using such normalized and -standardized files, multiple visualizations can be created to identify -enrichments with functional annotations of the genome. -For a gallery of images that can be produced and a description -of the tools see our poster_. - -.. _poster: http://f1000.com/posters/browse/summary/1094053 - -deeptools is developed under here: - - https://github.com/deeptools/deepTools - -For support or questions please post to `Biostars <http://biostars.org>`__. For bug reports and feature requests please open an issue `<on github <http://github.com/deeptools/deeptools>`__. - - -============ -Installation -============ - -Requirements: python-2.7 - -Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. - -For the best performance we recommend to install blas/lapack/atlas in your environment before -installing deepTools from the Tool Shed. - - -======== -Citation -======== - -deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools. - - -======= -History -======= - - * v1.0: Initial public release - * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version - - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE.
--- a/repository_dependencies.xml Sat Jan 25 05:11:38 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0" ?> -<repositories> - <repository changeset_revision="16c0c73b28ad" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/> -</repositories> \ No newline at end of file
--- a/test-data/bamPEFragmentSize_result1.txt Sat Jan 25 05:11:38 2020 -0500 +++ b/test-data/bamPEFragmentSize_result1.txt Thu May 18 20:45:20 2023 +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 Sat Jan 25 05:11:38 2020 -0500 +++ b/test-data/bamPEFragmentSize_table1.txt Thu May 18 20:45:20 2023 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBigwigSummary_result2.npz Thu May 18 20:45:20 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 May 18 20:45:20 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
--- a/test-data/plotFingerprint_quality_metrics.tabular Sat Jan 25 05:11:38 2020 -0500 +++ b/test-data/plotFingerprint_quality_metrics.tabular Thu May 18 20:45:20 2023 +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 Sat Jan 25 05:11:38 2020 -0500 +++ b/test-data/plotPCA_result2.tabular Thu May 18 20:45:20 2023 +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