Mercurial > repos > wolma > mimodd_coverage_stats
changeset 0:d831ac546bf7 draft
Imported from capsule None
| author | wolma |
|---|---|
| date | Sat, 13 Dec 2014 17:19:42 -0500 |
| parents | |
| children | fa6c970d07d7 |
| files | covstats.xml tool_dependencies.xml |
| diffstat | 2 files changed, 36 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/covstats.xml Sat Dec 13 17:19:42 2014 -0500 @@ -0,0 +1,30 @@ +<tool id="coverage_stats" name="Coverage Statistics"> + <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description> + <requirements> + <requirement type="package" version="0.1.5">mimodd</requirement> + </requirements> + <version_command>mimodd version -q</version_command> + <command> + mimodd covstats $ifile --ofile $output_vcf + </command> + + <inputs> + <param name="ifile" type="data" format="bcf" label="BCF input file" help="Use the Variant Calling tool to generate input for this tool."/> + </inputs> + <outputs> + <data name="output_vcf" format="tabular" label="Coverage Statistics for ${on_string}"/> + </outputs> + +<help> +.. class:: infomark + + **What it does** + +The tool takes as input a BCF file produced by the *Variant Calling* tool, and calculates per-chromosome read coverage from it. + +.. class:: warningmark + + 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. + +</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Dec 13 17:19:42 2014 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mimodd" version="0.1.5"> + <repository changeset_revision="fbac402764d6" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>