Mercurial > repos > bgruening > deeptools_plot_coverage

changeset 27:7fda5607e777 draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 9308cb7fc910dba348d48fd0dce77a90264b7bdb"
author bgruening
date Fri, 11 Feb 2022 15:16:22 +0000
parents 56bce3c82278
children 9368fbc49c8b
files deepTools_macros.xml plotCoverage.xml readme.rst 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 8 files changed, 8 insertions(+), 89 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Sat Jan 25 04:32:12 2020 -0500
+++ b/deepTools_macros.xml	Fri Feb 11 15:16:22 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	Sat Jan 25 04:32:12 2020 -0500
+++ b/plotCoverage.xml	Fri Feb 11 15:16:22 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/readme.rst	Sat Jan 25 04:32:12 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 04:32:12 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 04:32:12 2020 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt	Fri Feb 11 15:16:22 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	Sat Jan 25 04:32:12 2020 -0500
+++ b/test-data/bamPEFragmentSize_table1.txt	Fri Feb 11 15:16:22 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	Sat Jan 25 04:32:12 2020 -0500
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Feb 11 15:16:22 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	Sat Jan 25 04:32:12 2020 -0500
+++ b/test-data/plotPCA_result2.tabular	Fri Feb 11 15:16:22 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