# HG changeset patch
# User jbrayet
# Date 1448439749 18000
# Node ID 4b56f6feb24867fd0cda3e6e2ebb9c55dc4a325e
# Parent  8be7fb96589d1b6a176868ee89d92ef39ead2311
Uploaded

diff -r 8be7fb96589d -r 4b56f6feb248 samtools_flagstat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_flagstat.xml	Wed Nov 25 03:22:29 2015 -0500
@@ -0,0 +1,45 @@
+<tool id="samtools_flagstat" name="Flagstat" version="2.0">
+  <description>tabulate descriptive stats for BAM datset</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+  <command>samtools flagstat "$input1" > "$output1"
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="txt" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
+      <output name="output1" file="samtools_flagstat_out1.txt" />
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
+
+  200 + 0 in total (QC-passed reads + QC-failed reads)  
+  0 + 0 secondary
+  0 + 0 supplementary
+  0 + 0 duplicates
+  25 + 0 mapped (12.50%:nan%)
+  200 + 0 paired in sequencing
+  100 + 0 read1
+  100 + 0 read2
+  0 + 0 properly paired (0.00%:nan%)
+  0 + 0 with itself and mate mapped
+  25 + 0 singletons (12.50%:nan%)
+  0 + 0 with mate mapped to a different chr
+  0 + 0 with mate mapped to a different chr (mapQ>=5)
+  
+  </help>
+  <expand macro="citations"></expand>
+</tool>