changeset 3:6da6f2908463 draft

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

--- 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.
 

--- 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">

Binary file test-data/bamCoverage_result5.bw has changed

Binary file test-data/computeMatrix_result1.gz has changed

Binary file test-data/computeMatrix_result2.gz has changed

Binary file test-data/computeMatrix_result3.gz has changed

Binary file test-data/heatmapper_result1.png has changed

Binary file test-data/heatmapper_result2.png has changed

--- /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

Binary file test-data/plotCorrelation_result1.png has changed

Binary file test-data/plotCoverage_result1.png has changed

Binary file test-data/plotPCA_result1.png has changed

Binary file test-data/plotPCA_result2.png has changed

--- /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

Binary file test-data/profiler_result1.png has changed

Binary file test-data/profiler_result2.png has changed

--- /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