diff samtools_flagstat.xml @ 2:0072bf593791 draft

Uploaded

--- a/samtools_flagstat.xml	Thu Mar 27 15:23:45 2014 -0400
+++ b/samtools_flagstat.xml	Tue Apr 21 15:56:53 2015 -0400
@@ -1,8 +1,11 @@
-<tool id="samtools_flagstat" name="flagstat" version="1.0.1">
-  <requirements>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <description>provides simple stats on BAM files</description>
+<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>
@@ -13,7 +16,7 @@
   </outputs>
   <tests>
     <test>
-      <param name="input1" value="3unsorted.bam" ftype="bam" />
+      <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
       <output name="output1" file="samtools_flagstat_out1.txt" />
     </test>
   </tests>
@@ -21,17 +24,22 @@
 
 **What it does**
 
-This tool uses the SAMTools_ toolkit to produce simple stats on a BAM file.
-
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
-------
+Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
 
-**Citation**
-
-For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
+  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>