diff samtools_bedcov.xml @ 1:8c3472790020 draft

Uploaded

--- a/samtools_bedcov.xml	Wed Mar 18 16:43:50 2015 -0400
+++ b/samtools_bedcov.xml	Tue Apr 21 15:05:45 2015 -0400
@@ -1,11 +1,11 @@
-<tool id="samtools_bedcov" name="Calculate read depth" version="1.0.1">
-  <description>on BAM files</description>
+<tool id="samtools_bedcov" name="BedCov" version="2.0">
+  <description>calculate read depth for a set of genomic intervals</description>
   <macros>
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
     <expand macro="version_command"></expand>
-    <expand macro="stdio"></expand>
     <command><![CDATA[
         for bamfile in 
         #for dataset in $input_bams:
@@ -47,9 +47,9 @@
     <help>
 **What it does**
 
-This tool runs the ``samtools bedcov`` command in the SAMtools toolkit.
+Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
 
-Show read depth per BED region.
+ samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
 
     </help>
     <expand macro="citations"></expand>