# HG changeset patch
# User wolma
# Date 1418509182 18000
# Node ID d831ac546bf71d6a9c6db0c3c6d8dcd5cbdf0b3f

Imported from capsule None

diff -r 000000000000 -r d831ac546bf7 covstats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covstats.xml	Sat Dec 13 17:19:42 2014 -0500
@@ -0,0 +1,30 @@
+<tool id="coverage_stats" name="Coverage Statistics">
+  <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
+  <requirements>
+    <requirement type="package" version="0.1.5">mimodd</requirement>
+  </requirements>
+  <version_command>mimodd version -q</version_command>
+  <command> 
+	mimodd covstats $ifile --ofile $output_vcf
+  </command>
+
+  <inputs>
+      <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
+  </inputs>
+  <outputs>
+    <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
+  </outputs>
+
+<help>
+.. class:: infomark
+
+   **What it does**
+
+The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
+
+.. class:: warningmark
+
+   The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites.
+
+</help>
+</tool>
diff -r 000000000000 -r d831ac546bf7 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Dec 13 17:19:42 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="mimodd" version="0.1.5">
+      <repository changeset_revision="fbac402764d6" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>