# HG changeset patch
# User jeltje
# Date 1421091902 18000
# Node ID b469f90740f8d6d59115a98c9dc6786e19de1bb4
# Parent  a381e8c76e58991aae297b4b7220514c1dc7c29d
Uploaded

diff -r a381e8c76e58 -r b469f90740f8 samtools_flagstat.xml
--- a/samtools_flagstat.xml	Fri Jan 09 18:40:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-<tool id="samtools_0_1_18_flagstat" name="flagstat" version="1.0.0">
-  <requirements>
-      <requirement type="package" version="0.1.18">samtools</requirement>
-  </requirements>
-  <description>provides simple stats on BAM files</description>
-  <command>samtools flagstat "$input1" > "$output1"
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File" />
-  </inputs>
-  <outputs>
-    <data name="output1" format="txt" />
-  </outputs>
-<!--
-  <tests>
-    <test>
-      <param name="input1" value="unsorted.bam" ftype="bam" />
-      <output name="output1" file="samtools_flagstat_out1.txt" />
-    </test>
-  </tests>
--->
-  <help>
-
-This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file.
-
-  </help>
-</tool>
diff -r a381e8c76e58 -r b469f90740f8 samtools_mpileup.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_mpileup.xml	Mon Jan 12 14:45:02 2015 -0500
@@ -0,0 +1,37 @@
+<tool id="samtools_1_18_mpileup" name=mpileup" version="1.0.0">
+  <requirements>
+      <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <description>runs basic mpileup on input control and tumor files</description>
+  <command>samtools mpileup "$bamc" "$bamt"> "$output1"
+<!--
+  <command>samtools mpileup -q 1 -B "$index" "$bamc" "$bamt"> "$output1"
+-->
+  </command>
+  <inputs>
+    <param name="bamc" type="data" format="bam" label="BAM file (control)" />
+    <param name="bamt" type="data" format="bam" label="BAM file (tumor)" />
+<!--
+    <param name="index" type="select">
+    <options from_data_table="picard_index" />
+-->
+  </param>
+  </inputs>
+  <outputs>
+    <data name="output1" format="txt" />
+  </outputs>
+<!--
+  <tests>
+    <test>
+      <param name="input1" value="unsorted.bam" ftype="bam" />
+      <output name="output1" file="samtools_flagstat_out1.txt" />
+    </test>
+  </tests>
+-->
+  <help>
+
+This tool runs the mpileup command of samtools 0.1.18
+with flags -q 1 -B
+
+  </help>
+</tool>