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comparison covstats.xml @ 0:d831ac546bf7 draft

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Imported from capsule None
author wolma
date Sat, 13 Dec 2014 17:19:42 -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 <requirements>
4 <requirement type="package" version="0.1.5">mimodd</requirement>
5 </requirements>
6 <version_command>mimodd version -q</version_command>
7 <command>
8 mimodd covstats $ifile --ofile $output_vcf
9 </command>
10
11 <inputs>
12 <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
13 </inputs>
14 <outputs>
15 <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
16 </outputs>
17
18 <help>
19 .. class:: infomark
20
21 **What it does**
22
23 The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
24
25 .. class:: warningmark
26
27 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.
28
29 </help>
30 </tool>