|
5
|
1 <tool id="coverage_stats" name="Coverage Statistics" version="0.1.6.1">
|
|
0
|
2 <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
|
|
2
|
3 <macros>
|
|
|
4 <import>toolshed_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements"/>
|
|
0
|
7 <version_command>mimodd version -q</version_command>
|
|
|
8 <command>
|
|
|
9 mimodd covstats "$ifile" --ofile "$output_vcf"
|
|
|
10 </command>
|
|
|
11
|
|
|
12 <inputs>
|
|
|
13 <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/>
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/>
|
|
|
17 </outputs>
|
|
|
18
|
|
|
19 <help>
|
|
|
20 .. class:: infomark
|
|
|
21
|
|
|
22 **What it does**
|
|
|
23
|
|
|
24 The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it.
|
|
|
25
|
|
|
26 .. class:: warningmark
|
|
|
27
|
|
|
28 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.
|
|
|
29
|
|
|
30 </help>
|
|
|
31 </tool>
|
