Mercurial > repos > jeltje > samtools_1_18_mpileup

changeset 9:97b524d88b36 draft

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Uploaded
author jeltje
date Mon, 12 Jan 2015 14:59:48 -0500
parents 48161d4bd762
children c60f33b42a20
files samtools_mpileup.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_mpileup.xml	Mon Jan 12 14:57:42 2015 -0500
+++ b/samtools_mpileup.xml	Mon Jan 12 14:59:48 2015 -0500
@@ -1,13 +1,13 @@
-<tool id="samtools_0_1_18_mpileup" name="mpileup" version="1.0.0">
+<tool id="samtools_1_18_mpileup" name="mpileup" version="1.0.0">
   <requirements>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description>creates mpileup for VarScan2</description>
-  <command>samtools mpileup -q 1 -B "$input1" "$input2" > "$output1"
+  <command>samtools mpileup -q 1 -B "$bamc" "$bamt" > "$output1"
   </command>
   <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File" />
-    <param name="input2" type="data" format="bam" label="BAM File" />
+    <param name="bamc" type="data" format="bam" label="BAM File" />
+    <param name="bamt" type="data" format="bam" label="BAM File" />
   </inputs>
   <outputs>
     <data name="output1" format="txt" />