Mercurial > repos > wolma > mimodd
annotate covstats.xml @ 21:c46406466625 draft
Uploaded
| author | wolma |
|---|---|
| date | Sat, 11 Jun 2016 19:10:44 -0400 |
| parents | 93db2f9bca12 |
| children | 5db0545b9004 |
| rev | line source |
|---|---|
|
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"/> | |
| 21 | 7 <version_command>python3 -m MiModD version -q</version_command> |
| 0 | 8 <command> |
| 21 | 9 python3 -m MiModD covstats "$ifile" --ofile "$output_vcf" |
| 0 | 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> |