Mercurial > repos > wolma > mimodd
annotate covstats.xml @ 18:2742ad4d1608 draft
rebase on package_python_3_4_lean
author | wolma |
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date | Tue, 26 Apr 2016 11:21:43 -0400 |
parents | 93db2f9bca12 |
children | c46406466625 |
rev | line source |
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9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
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1 <tool id="coverage_stats" name="Coverage Statistics" version="0.1.7.2"> |
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> |