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diff junction_saturation.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_saturation.xml	Wed Oct 02 02:20:04 2013 -0400
+++ b/junction_saturation.xml	Mon Oct 07 15:01:13 2013 -0400
@@ -1,40 +1,40 @@
-<tool id="junction_saturation" name="Junction Saturation" version="1.1">
-	<description>detects splice junctions from each subset and compares them 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_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
-
-		#if $percentiles.specifyPercentiles
-			-l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
-		#end if
+<tool id="rseqc_junction_saturation" name="Junction Saturation" version="1.1">
+    <description>detects splice junctions from each subset and compares them 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_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
 
-	</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" />
-		<param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
-		<param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="1" />
-		<conditional name="percentiles">
-			<param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
-			<when value="true">
-				<param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
-				<param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
-				<param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
-			</when>
-		</conditional>
-	</inputs>
-	<outputs>
-		<data format="r" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
-		<data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
-	</outputs>
+        #if $percentiles.specifyPercentiles
+            -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
+        #end if
+
+    </command>
     <stdio>
         <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
         <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
     </stdio>
-	<help>
+    <inputs>
+        <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
+        <param name="refgene" type="data" format="bed" label="reference gene model" />
+        <param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
+        <param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="1" />
+        <conditional name="percentiles">
+            <param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
+            <when value="true">
+                <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
+                <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
+                <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
+        <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
+    </outputs>
+    <help>
 junction_saturation.py
 ++++++++++++++++++++++
 
@@ -52,19 +52,19 @@
 ++++++++++++++
 
 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.
 
 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5)
-	Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
+    Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
 
 Minimum intron length (default=50)
-	Minimum intron length (bp).
+    Minimum intron length (bp).
 
 Minimum coverage (default=1)
-	Minimum number of supportting reads to call a junction.
+    Minimum number of supportting reads to call a junction.
 
 Output
 ++++++++++++++
@@ -95,5 +95,5 @@
 
 
 
-	</help>
+    </help>
 </tool>