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comparison covstats.xml @ 0:6231ae8f87b8

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author wolma
date Wed, 11 Feb 2015 08:29:02 -0500
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1 <tool id="coverage_stats" name="Coverage Statistics">
2 <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
3 <version_command>mimodd version -q</version_command>
4 <command>
5 mimodd covstats "$ifile" --ofile "$output_vcf"
6 </command>
7
8 <inputs>
9 <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
10 </inputs>
11 <outputs>
12 <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
13 </outputs>
14
15 <help>
16 .. class:: infomark
17
18 **What it does**
19
20 The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
21
22 .. class:: warningmark
23
24 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.
25
26 </help>
27 </tool>