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changeset 51:6a2a7374450b

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Uploaded
author bgruening
date Fri, 02 Aug 2013 13:53:20 -0400
parents f9390e176b8f
children 411c871f4cfd
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml profiler.xml
diffstat 9 files changed, 23 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/bamCompare.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,6 +1,7 @@
 <tool id="bamCompare" name="bamCompare" version="1.0">
   <description>Normalize and compare two BAM files to output ratio, log2ratio or difference.</description>
   <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="python-module">argsparse</requirement>
     <requirement type="python-module">pysam</requirement>
--- a/bamCorrelate.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/bamCorrelate.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,6 +1,8 @@
 <tool id="bamCorrelate" name="bamCorrelate" version="1.0">
   <description>corrlates pairs of bam files</description>
-
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   #set files=[]
   #set labels=[]
--- a/bamCoverage.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/bamCoverage.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,10 +1,8 @@
 <tool id="bamCoverage" name="bamCoverage" version="1.0">
   <description>Given a BAM file, generates a coverage bigwig file.  Multiple options available to count reads and normalize coverage.</description>
   <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
-    <requirement type="python-module">argsparse</requirement>
-    <requirement type="python-module">pysam</requirement>
-    <requirement type="python-module">numpy</requirement>
   </requirements>
   <command>bamCoverage
   --bam '$bamInput'
--- a/bamFingerprint.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/bamFingerprint.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,6 +1,8 @@
 <tool id="bamFingerprint" name="bamFingerprint" version="1.0">
   <description>plots profiles of bam files</description>
-
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   #set files=[]
   #set labels=[]
--- a/bigwigCompare.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/bigwigCompare.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,6 +1,8 @@
 <tool id="bigwigCompare" name="bigwigCompare" version="1.0">
   <description>compares two bigwig files based on the number of mapped reads</description>
-
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   bigwigCompare
   --bigwig1 '$bigwigFile1'
--- a/computeGCBias.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/computeGCBias.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,5 +1,8 @@
 <tool id="computeGCBias" name="computeGCBias" version="1.0">
   <description></description>
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <stdio>
     <exit_code range="0" level="warning" description="Warning" />
   </stdio>
--- a/computeMatrix.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/computeMatrix.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,5 +1,8 @@
 <tool id="computeMatrix" name="computeMatrix" version="1.0">
   <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   computeMatrix
   $mode.mode_select
--- a/correctGCBias.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/correctGCBias.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -1,6 +1,9 @@
 <tool id="correctGCBias" name="correctGCBias" version="1.0">
   <description>
   </description>
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   correctGCBias
   --bamfile '$bamInput'
--- a/profiler.xml	Fri Aug 02 12:54:19 2013 -0400
+++ b/profiler.xml	Fri Aug 02 13:53:20 2013 -0400
@@ -2,7 +2,9 @@
   <description>
     creates a profile plot for a score associated to genomic regions
   </description>
-
+  <requirements>
+    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+  </requirements>
   <command>
   profiler
   --matrixFile $matrixFile