# HG changeset patch
# User p.lucas
# Date 1718267547 0
# Node ID 7bcef9bf4f18be87585d650f40f1bde37e936f7f
# Parent  5558479694c793d13963beef4270036f4c47882d
Uploaded wrapper

diff -r 5558479694c7 -r 7bcef9bf4f18 graph_coverage_multi_png.xml
--- /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>
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