diff read_NVC.xml @ 32:580ee0c4bc4e

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

--- a/read_NVC.xml	Wed Oct 02 02:20:04 2013 -0400
+++ b/read_NVC.xml	Mon Oct 07 15:01:13 2013 -0400
@@ -1,30 +1,27 @@
-<tool id="read_NVC" name="Read NVC" version="1.1">
-	<description>to check the nucleotide composition bias</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> read_NVC.py -i $input -o output
-
-		#if $nx
-			-x
-		#end if
-	</command>
-	<inputs>
-		<param name="input" type="data" format="bam,sam" label="input bam/sam file" />
-		<param name="nx" type="boolean" label="Include N,X in NVC plot" value="false" />
-	</inputs>
-	<outputs>
-		<data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
-		<data format="r" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
-		<data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
-	</outputs>
+<tool id="rseqc_read_NVC" name="Read NVC" version="1.1">
+    <description>to check the nucleotide composition bias</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>
+        read_NVC.py -i $input -o output $nx
+    </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
         <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
     </stdio>
-	<help>
+    <inputs>
+        <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
+        <param name="nx" type="boolean" value="false" truevalue="-x" falsevalue="" label="Include N,X in NVC plot"/>
+    </inputs>
+    <outputs>
+        <data format="xls" name="outputxls" from_work_dir="output.NVC.xls" label="${tool.name} on ${on_string} (XLS)" />
+        <data format="txt" name="outputr" from_work_dir="output.NVC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
+        <data format="pdf" name="outputpdf" from_work_dir="output.NVC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
+    </outputs>
+    <help>
 read_NVC.py
 +++++++++++
 
@@ -41,10 +38,10 @@
 ++++++++++++++
 
 Input BAM/SAM file
-	Alignment file in BAM/SAM format.
+    Alignment file in BAM/SAM format.
 
 Include N,X in NVC plot
-	Plots N and X alongside A, T, C, and G in plot.
+    Plots N and X alongside A, T, C, and G in plot.
 
 Output
 ++++++++++++++
@@ -76,5 +73,5 @@
 .. _RSeQC: http://rseqc.sourceforge.net/
 
 
-	</help>
+    </help>
 </tool>