Galaxy |

Changeset 3:6da6f2908463 (2016-03-09)

Previous changeset 2:ef131d53cbdf (2016-02-18) Next changeset 4:1a34ad2f4704 (2016-03-10)

Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

modified:
bamPEFragmentSize.xml
deepTools_macros.xml
test-data/computeMatrix_result1.gz
test-data/computeMatrix_result2.gz
test-data/computeMatrix_result3.gz
test-data/heatmapper_result1.png
test-data/heatmapper_result2.png
test-data/plotCorrelation_result1.png
test-data/plotCoverage_result1.png
test-data/plotPCA_result1.png
test-data/profiler_result1.png
test-data/profiler_result2.png

added:
test-data/bamCoverage_result5.bw
test-data/heatmapper_result2.tabular
test-data/plotPCA_result2.png
test-data/plotPCA_result2.tabular
test-data/profiler_result2.tabular

diff -r ef131d53cbdf -r 6da6f2908463 bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml Thu Feb 18 11:42:40 2016 -0500
+++ b/bamPEFragmentSize.xml Wed Mar 09 17:49:50 2016 -0500

[

@@ -26,7 +26,7 @@
     </command>
     <inputs>
         <param name="bamInput" format="bam" type="data" label="BAM file"
-            help="The BAM file must be sorted."/>
+            help=""/>
         <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue=""
             label="Get the distribution of fragment lengths as a histogram"
             help=""/>
@@ -66,13 +66,13 @@
<![CDATA[

What it does
----------------
+------------

This tool samples a BAM file with paired-end data to estimate the fragment length distribution.
Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored.

Output
-----------
+------

The **default** output is a simple summary statistic for the observed fragment lengths.

diff -r ef131d53cbdf -r 6da6f2908463 deepTools_macros.xml
--- a/deepTools_macros.xml Thu Feb 18 11:42:40 2016 -0500
+++ b/deepTools_macros.xml Wed Mar 09 17:49:50 2016 -0500

@@ -72,12 +72,12 @@
     </xml>

     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.1.0</token>
+    <token name="@WRAPPER_VERSION@">2.2.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.1.0">deepTools</requirement>
+            <requirement type="package" version="2.2.2">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -310,13 +310,13 @@
     <xml name="multiple_input_bams">
         <param argument="--bamfiles" type="data" format="bam" min="1"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>

     <xml name="multiple_input_bams_min2">
         <param argument="--bamfiles" type="data" format="bam" min="2"
             label="Bam file" multiple="true"
-            help="The BAM file must be sorted."/>
+            help=""/>
     </xml>

     <xml name="multiple_input_bigwigs">

diff -r ef131d53cbdf -r 6da6f2908463 test-data/bamCoverage_result5.bw

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/computeMatrix_result1.gz

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/computeMatrix_result2.gz

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/computeMatrix_result3.gz

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/heatmapper_result1.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/heatmapper_result2.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/heatmapper_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/heatmapper_result2.tabular Wed Mar 09 17:49:50 2016 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234

diff -r ef131d53cbdf -r 6da6f2908463 test-data/plotCorrelation_result1.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/plotCoverage_result1.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/plotPCA_result1.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/plotPCA_result2.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/plotPCA_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotPCA_result2.tabular Wed Mar 09 17:49:50 2016 -0500

@@ -0,0 +1,3 @@
+Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
+1 -0.707106781187 -0.707106781187 6.0
+2 -0.707106781187 0.707106781187 1.23259516441e-32

diff -r ef131d53cbdf -r 6da6f2908463 test-data/profiler_result1.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/profiler_result2.png

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diff -r ef131d53cbdf -r 6da6f2908463 test-data/profiler_result2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profiler_result2.tabular Wed Mar 09 17:49:50 2016 -0500

@@ -0,0 +1,3 @@
+bin labels -0.0Kb 0.0Kb
+bins 1 2
+file_0 genes 2477942.34473 2610259.65234