diff varscan_mpileup.xml @ 2:d062703d6f13 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
author iuc
date Tue, 04 Dec 2018 05:16:18 -0500
parents 1e667badbe87
children
line wrap: on
line diff
--- a/varscan_mpileup.xml	Sun Jul 15 09:19:37 2018 -0400
+++ b/varscan_mpileup.xml	Tue Dec 04 05:16:18 2018 -0500
@@ -1,9 +1,11 @@
-<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0">
+<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.1">
     <description>for variant detection</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="4.2.1">gawk</requirement>
+    </expand>
     <expand macro="stdio" />
     <command><![CDATA[
         ## Set up samples list file.
@@ -74,16 +76,8 @@
         </test>
     </tests>
 
-    <help>
-**VarScan Overview**
-
-VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
-It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
-
-This tool detects variants from pileups.
-
-.. _VarScan: http://dkoboldt.github.io/varscan/
-.. _online: http://dkoboldt.github.io/varscan/using-varscan.html
+    <help><![CDATA[
+@HELP_HEADER@
 
 **Input**
 
@@ -96,6 +90,6 @@
 
 VarScan produces a VCF 4.1 dataset as output.
 
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>