Mercurial > repos > p.lucas > get_coverage_graph
changeset 1:7bcef9bf4f18 draft default tip
Uploaded wrapper
| author | p.lucas |
|---|---|
| date | Thu, 13 Jun 2024 08:32:27 +0000 |
| parents | 5558479694c7 |
| children | |
| files | graph_coverage_multi_png.xml |
| diffstat | 1 files changed, 34 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graph_coverage_multi_png.xml Thu Jun 13 08:32:27 2024 +0000 @@ -0,0 +1,34 @@ +<tool id="get_cov_graph" name="get graph of coverage depth" version="1.16"> + <description> + From coverage file (after samtools depth with "-a -d 0" option), get graph for each reference used in the alignment. + </description> + <requirements> + <requirement type="package" version="4.1">r</requirement> + <requirement type="package" version="0.8.9">r-reshape</requirement> + <requirement type="package" version="3.3.6">r-ggplot2</requirement> + <requirement type="package" version="1.4.1">r-stringr</requirement> + <requirement type="package" version="2.3">r-gridextra</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + mkdir -p graph_cov; + Rscript '$__tool_directory__/graph_coverage_multi_png.R' "$depth_file" graph_cov/coverage_graph.png + ]]></command> + <inputs> + <param name="depth_file" type="data" format="tabular" label="Depth file" help="Output from samtools depth command"/> + </inputs> + <outputs> + <collection name="output" type="list" label="Unknown number of graph files" > + <discover_datasets pattern="__designation_and_ext__" directory="graph_cov" ext="png"/> + </collection> + </outputs> + <help> + <![CDATA[ + +Homemade script to get one coverage graphe by reference of alignment. +If you have more than 8 reference in reference file, others files will be created. + ]]> + </help> +</tool> \ No newline at end of file