# HG changeset patch
# User jeltje
# Date 1421091077 18000
# Node ID 41c4eb01c566a0d658a4ecde705080763080d0ae

Uploaded

diff -r 000000000000 -r 41c4eb01c566 samtools_mpileup.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_mpileup.xml	Mon Jan 12 14:31:17 2015 -0500
@@ -0,0 +1,32 @@
+<tool id="samtools_0_1_18mpileup" 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 -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>
diff -r 000000000000 -r 41c4eb01c566 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 12 14:31:17 2015 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.18">
+        <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>