Mercurial > repos > bgruening > deeptools_plot_fingerprint

changeset 3:d0c03d57e471 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c
author bgruening
date Wed, 09 Mar 2016 17:56:38 -0500
parents 91b340ca9e92
children dd7c02c4b33a
files deepTools_macros.xml plotFingerprint.xml test-data/bamCoverage_result5.bw 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/heatmapper_result2.tabular test-data/plotCorrelation_result1.png test-data/plotCoverage_result1.png test-data/plotPCA_result1.png test-data/plotPCA_result2.png test-data/plotPCA_result2.tabular test-data/profiler_result1.png test-data/profiler_result2.png test-data/profiler_result2.tabular
diffstat 17 files changed, 16 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Thu Feb 18 11:44:30 2016 -0500
+++ b/deepTools_macros.xml	Wed Mar 09 17:56:38 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">
--- a/plotFingerprint.xml	Thu Feb 18 11:44:30 2016 -0500
+++ b/plotFingerprint.xml	Wed Mar 09 17:56:38 2016 -0500
@@ -114,14 +114,14 @@
 
 
 What it does
----------------
+------------
 
 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
 
 
 Output
----------
+------
 
 The default output is a diagnostic plot (see below for an example and further down for some background information).
 
@@ -142,7 +142,7 @@
    :width: 600
    :height: 450
 
------------------------------
+-----
 
 Theoretical Background
 ----------------------
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 17:56:38 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 17:56:38 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 17:56:38 2016 -0500
@@ -0,0 +1,3 @@
+bin labels		-0.0Kb	0.0Kb
+bins		1	2
+file_0	genes	2477942.34473	2610259.65234