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diff junction_annotation.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/junction_annotation.xml	Wed Oct 02 02:20:04 2013 -0400
+++ b/junction_annotation.xml	Mon Oct 07 15:01:13 2013 -0400
@@ -1,38 +1,38 @@
-<tool id="junction_annotation" name="Junction Annotation" version="1.1">
-	<description>compares detected splice junctions to reference gene model</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> junction_annotation.py -i $input -o output -r $refgene
-
-		#if $intron.hasIntron
-			-m $intron.min_Intron
-		#end if
-
-	</command>
-	<inputs>
-		<param name="input" type="data" format="bam,sam" label="input bam/sam file" />
-		<param name="refgene" type="data" format="bed" label="reference gene model" />
-		<conditional name="intron">
-			<param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
-			<when value="true">
-				<param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
-			</when>
-		</conditional>
-	</inputs>
-	<outputs>
-		<data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
-		<data format="r" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
-		<data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
-		<data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
-	</outputs>
+<tool id="rseqc_junction_annotation" name="Junction Annotation" version="1.1">
+    <description>compares detected splice junctions to reference gene model</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>
+        junction_annotation.py 
+            -i $input -o output -r $refgene
+            #if $intron.hasIntron
+                -m $intron.min_Intron
+            #end if
+    </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
         <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
     </stdio>
-	<help>
+    <inputs>
+        <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
+        <param name="refgene" type="data" format="bed" label="reference gene model" />
+        <conditional name="intron">
+            <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
+            <when value="true">
+                <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
+        <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
+        <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
+        <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
+    </outputs>
+    <help>
 junction_annotation.py
 ++++++++++++++++++++++
 
@@ -54,13 +54,13 @@
 ++++++++++++++
 
 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.
 
 Minimum intron length (default=50)
-	Minimum intron length (bp).
+    Minimum intron length (bp).
 
 
 Output
@@ -97,5 +97,5 @@
 
 
 
-	</help>
+    </help>
 </tool>