# HG changeset patch
# User bgruening
# Date 1474355127 14400
# Node ID 1bd89a520120ecc48c020d67241f202867adf48a
# Parent 610bbc25ed8b9f2d4c0085d98a3e9aecc394b954
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
diff -r 610bbc25ed8b -r 1bd89a520120 deepTools_macros.xml
--- a/deepTools_macros.xml Fri May 13 14:31:15 2016 -0400
+++ b/deepTools_macros.xml Tue Sep 20 03:05:27 2016 -0400
@@ -30,6 +30,25 @@
#if $advancedOpt.samFlagExclude:
--samFlagExclude $advancedOpt.samFlagExclude
#end if
+ #if $advancedOpt.minFragmentLength:
+ --minFragmentLength $advancedOpt.minFragmentLength
+ #end if
+ #if $advancedOpt.maxFragmentLength:
+ --maxFragmentLength $advancedOpt.maxFragmentLength
+ #end if
+
+
+
+ $advancedOpt.metagene
+ #if $advancedOpt.transcriptID:
+ --transcriptID $advancedOpt.transcriptID
+ #end if
+ #if $advancedOpt.exonID:
+ --exonID $advancedOpt.exonID
+ #end if
+ #if $advancedOpt.transcript_id_designator:
+ --transcript_id_designator $advancedOpt.transcript_id_designator
+ #end if
@@ -59,9 +78,9 @@
-
-
@@ -72,18 +91,18 @@
+
--numberOfProcessors "\${GALAXY_SLOTS:-4}"
- 2.2.3
+ 2.3.5
python
- @BINARY@
- deepTools
+ deepTools
@@ -159,14 +178,43 @@
help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
@@ -363,6 +411,47 @@
]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0:
+ --BED #echo ' '.join($files)#
+ --regionLabels #echo ' '.join($labels)#
+ #end if
+]]>
+
+
@@ -404,7 +493,8 @@
-
+
@@ -439,7 +529,10 @@
-
+
@@ -454,6 +547,11 @@
+
+
+
+
@@ -497,7 +595,9 @@
-
+
diff -r 610bbc25ed8b -r 1bd89a520120 static/images/plotEnrichment_output.png
Binary file static/images/plotEnrichment_output.png has changed
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCompare_result1.bg
--- a/test-data/bamCompare_result1.bg Fri May 13 14:31:15 2016 -0400
+++ b/test-data/bamCompare_result1.bg Tue Sep 20 03:05:27 2016 -0400
@@ -1,1 +1,1 @@
-chrM 0 16569 1.0
+chrM 0 16569 1.00
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg Fri May 13 14:31:15 2016 -0400
+++ b/test-data/bamCoverage_result3.bg Tue Sep 20 03:05:27 2016 -0400
@@ -1,8 +1,7 @@
-chrM 0 10 18498299.57
-chrM 10 200 9768764.94
-chrM 200 210 10184457.07
-chrM 210 220 9976611.00
+chrM 0 210 9768764.94
+chrM 210 220 9560918.88
chrM 220 230 7690304.31
-chrM 230 240 6027535.81
+chrM 230 240 5196151.56
chrM 240 250 3325537.00
chrM 250 260 623538.19
+chrM 260 16569 0.00
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg Fri May 13 14:31:15 2016 -0400
+++ b/test-data/bamCoverage_result4.bg Tue Sep 20 03:05:27 2016 -0400
@@ -1,472 +1,472 @@
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diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result4.bw
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diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamCoverage_result5.bw
Binary file test-data/bamCoverage_result5.bw has changed
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamPEFragmentSize_histogram_result1.png
Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 14:31:15 2016 -0400
+++ b/test-data/bamPEFragmentSize_result1.txt Tue Sep 20 03:05:27 2016 -0400
@@ -1,6 +1,8 @@
+
+
+BAM file : 0.bam
Sample size: 3
-
Fragment lengths:
Min.: 241.0
1st Qu.: 241.5
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/correctGCBias_result1.bam
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diff -r 610bbc25ed8b -r 1bd89a520120 test-data/plotEnrichment_output.png
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diff -r 610bbc25ed8b -r 1bd89a520120 test-data/plotEnrichment_output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotEnrichment_output.txt Tue Sep 20 03:05:27 2016 -0400
@@ -0,0 +1,5 @@
+file featureType percent
+bowtie2 test1.bam down 100.00
+bowtie2 test1.bam up 100.00
+bowtie2 test1.bam down 100.00
+bowtie2 test1.bam up 100.00
diff -r 610bbc25ed8b -r 1bd89a520120 test-data/plotFingerprint_result2.tabular
--- a/test-data/plotFingerprint_result2.tabular Fri May 13 14:31:15 2016 -0400
+++ b/test-data/plotFingerprint_result2.tabular Tue Sep 20 03:05:27 2016 -0400
@@ -1,239 +1,239 @@
'bowtie2 test1.bam' 'bowtie2 test1.bam'
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diff -r 610bbc25ed8b -r 1bd89a520120 tool_dependencies.xml
--- a/tool_dependencies.xml Fri May 13 14:31:15 2016 -0400
+++ b/tool_dependencies.xml Tue Sep 20 03:05:27 2016 -0400
@@ -3,7 +3,7 @@
-
-
+
+