# HG changeset patch
# User jeltje
# Date 1420846834 18000
# Node ID a381e8c76e58991aae297b4b7220514c1dc7c29d

Uploaded

diff -r 000000000000 -r a381e8c76e58 samtools_flagstat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_flagstat.xml	Fri Jan 09 18:40:34 2015 -0500
@@ -0,0 +1,27 @@
+<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 000000000000 -r a381e8c76e58 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jan 09 18:40:34 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>