diff covstats.xml @ 3:d6ec32ce882b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covstats.xml	Tue Mar 28 04:34:04 2017 -0400
@@ -0,0 +1,31 @@
+<tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.3">
+  <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command>mimodd version -q</version_command>
+  <command> 
+	mimodd covstats "$ifile" --ofile "$output_vcf"
+  </command>
+
+  <inputs>
+      <param format="bcf" help="Use the Variant Calling tool to generate input for this tool." label="BCF input file" name="ifile" type="data" />
+  </inputs>
+  <outputs>
+    <data format="tabular" label="Coverage Statistics for ${on_string}" name="output_vcf" />
+  </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>