Mercurial > repos > bgruening > deeptools_compute_matrix_operations

changeset 16:39ba04eacd0f draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit ac42d29c298c026aa0c53c9db2553087ebc86b97"
author bgruening
date Fri, 11 Feb 2022 10:02:59 +0000
parents f9a231be10dc
children 42402233f300
files computeMatrixOperations.xml deepTools_macros.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, 20 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/computeMatrixOperations.xml	Fri Jan 24 09:34:29 2020 +0000
+++ b/computeMatrixOperations.xml	Fri Feb 11 10:02:59 2022 +0000
@@ -71,6 +71,10 @@
                 -m $submodule.matrixFile
                 -R '#echo "' '".join($files)#'
                 -o $outFileName
+            #else if $submodule.command == "dataRange":
+                dataRange
+                -m $submodule.matrixFile
+                > $outFileTxt
             #end if
 ]]>
     </command>
@@ -85,6 +89,7 @@
                 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
                 <option value="cbind">Bind matrices, left to right (cbind)</option>
                 <option value="sort">Sort by region order in specified files (sort)</option>
+                <option value="dataRange">Returns the min, max, median, 10th and 90th percentile of the matrix values per sample (dataRange)</option>
             </param>
             <when value="info">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
@@ -151,6 +156,11 @@
                         help="File, in BED format, containing the regions to plot."/>
                 </repeat>
             </when>
+
+            <when value="dataRange">
+                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+                       label="Matrix file from the computeMatrix tool" help=""/>
+            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -205,7 +215,8 @@
 +----------------+--------------------------------------------------------------------------------------------------------------------------+
 + sort           | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s).                              |
 +----------------+--------------------------------------------------------------------------------------------------------------------------+
-
++ dataRange      | Returns the min, max, median, 10th and 90th percentile of the matrix values per sample.                                  |
++----------------+--------------------------------------------------------------------------------------------------------------------------+
 
 These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file.
 
--- a/deepTools_macros.xml	Fri Jan 24 09:34:29 2020 +0000
+++ b/deepTools_macros.xml	Fri Feb 11 10:02:59 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/repository_dependencies.xml	Fri Jan 24 09:34:29 2020 +0000
+++ b/repository_dependencies.xml	Fri Feb 11 10:02:59 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 09:34:29 2020 +0000
+++ b/test-data/bamPEFragmentSize_result1.txt	Fri Feb 11 10:02:59 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 09:34:29 2020 +0000
+++ b/test-data/bamPEFragmentSize_table1.txt	Fri Feb 11 10:02:59 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 09:34:29 2020 +0000
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Feb 11 10:02:59 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 09:34:29 2020 +0000
+++ b/test-data/plotPCA_result2.tabular	Fri Feb 11 10:02:59 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