Mercurial > repos > pitagora > gatk_1_6_pitagora

changeset 1:9b55ddff33e2

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commit
author pitagora <ryota.yamanaka@riken.jp>
date Wed, 15 Apr 2015 18:48:30 +0900
parents 5bad325a92d7
children 855b279dbdaf
files GATKRealignerTargetCreator.xml
diffstat 1 files changed, 31 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/GATKRealignerTargetCreator.xml	Wed Apr 15 18:41:05 2015 +0900
+++ b/GATKRealignerTargetCreator.xml	Wed Apr 15 18:48:30 2015 +0900
@@ -1,33 +1,34 @@
 <tool id="GATK_realigner_target_creator" name="GATK Realigner Target Creator" version="1.6.13">
-	<description></description>
-	<command interpreter="python">
-		GATKRealignerTargetCreator.py
-			--I $input
-			--O $output
-			--L $db_beds
-			--R $db_refgenomes
-			--nt $nt
-			--log $log
-	</command>
-	<requirements>
-	        <requirement type="package" version="1.6.13">gatk</requirement>
-	        <requirement type="package" version="0.1.19">samtools</requirement>
-	</requirements>
-	<inputs>
-		<param type="data" name="input" format="bam" label="Input file" />
-		<param type="integer" name="nt" value="0" label="processes num [-nt]" help="" />
-		<param type="select" name="db_beds" label="bed file [-L]">
-			<options from_data_table="gatk_beds" />
-		</param>
-		<param type="select" name="db_refgenomes" label="reference genome [-R]">
-			<options from_data_table="gatk_refgenomes" />
-		</param>
-	</inputs>
-	<outputs>
-		<data format="gatk_interval" name="output" />
-		<data format="txt" name="log" />
-	</outputs>
-	<help>
-	</help>
+  <description>for pitagora</description>
+  <command interpreter="python">
+    GATKRealignerTargetCreator.py
+      --I $input
+      --O $output
+      --L $db_beds
+      --R $db_refgenomes
+      --nt $nt
+      --log $log
+  </command>
+  <requirements>
+    <requirement type="package" version="1.6.13">gatk</requirement>
+    <requirement type="package" version="0.1.19">samtools</requirement>
+  </requirements>
+  <inputs>
+    <param type="data" name="input" format="bam" label="Input file" />
+    <param type="integer" name="nt" value="0" label="processes num [-nt]" help="" />
+    <param type="select" name="db_beds" label="bed file [-L]">
+      <options from_data_table="gatk_beds" />
+    </param>
+    <param type="select" name="db_refgenomes" label="reference genome [-R]">
+      <options from_data_table="gatk_refgenomes" />
+    </param>
+  </inputs>
+  <outputs>
+    <data format="gatk_interval" name="output" />
+    <data format="txt" name="log" />
+  </outputs>
+  <help>
+    help
+  </help>
 </tool>