diff samtools_flagstat.xml @ 2:1bf4de6596f1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_flagstat.xml	Mon Jan 12 14:46:55 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>