Mercurial > repos > nilesh > rseqc

diff geneBody_coverage2.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
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--- a/geneBody_coverage2.xml	Wed Oct 02 02:20:04 2013 -0400
+++ b/geneBody_coverage2.xml	Mon Oct 07 15:01:13 2013 -0400
@@ -1,29 +1,29 @@
-<tool id="geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="1.1">
-	<description>
-		Read coverage over gene body.
-	</description>
-	<requirements>
-		<requirement type="package" version="2.11.0">R</requirement>
-		<requirement type="package" version="1.7.1">numpy</requirement>
-		<requirement type="package" version="2.3.7">rseqc</requirement>
-	</requirements>
-	<command>
-		geneBody_coverage2.py -i $input -r $refgene -o output
-	</command>
-	<inputs>
-		<param name="input" type="data" label="Input bigwig file" format="bigwig" />
-		<param name="refgene" type="data" label="Reference Genome" format="bed" />
-	</inputs>
-	<outputs>
-		<data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
-		<data name="outputr" format="r" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
-		<data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
-    </outputs>
+<tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="1.1">
+    <description>
+        Read coverage over gene body
+    </description>
+    <requirements>
+        <requirement type="package" version="3.0.1">R</requirement>
+        <requirement type="package" version="1.7.1">numpy</requirement>
+        <requirement type="package" version="2.3.7">rseqc</requirement>
+    </requirements>
+    <command>
+        geneBody_coverage2.py -i $input -r $refgene -o output
+    </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
         <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
     </stdio>
-	<help>
+    <inputs>
+        <param name="input" type="data" label="Input bigwig file" format="bigwig" />
+        <param name="refgene" type="data" label="Reference Genome" format="bed" />
+    </inputs>
+    <outputs>
+        <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
+        <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
+        <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
+    </outputs>
+    <help>
 geneBody_coverage2.py
 +++++++++++++++++++++
 
@@ -35,10 +35,10 @@
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
 Reference gene model
-	Gene Model in BED format.
+    Gene Model in BED format.
 
 
 Outputs
@@ -67,5 +67,5 @@
 
 
 
-	</help>
+    </help>
 </tool>