# HG changeset patch
# User thanhlv
# Date 1570557270 14400
# Node ID ef0187f2d1f6bc8f6212103413c3f86506a96ce8

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/coverm commit a0be3607cd2a8b0d3bf6cdab4c9c50703936f941

diff -r 000000000000 -r ef0187f2d1f6 coverm.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverm.xml	Tue Oct 08 13:54:30 2019 -0400
@@ -0,0 +1,35 @@
+<tool id="coverm" name="coverm" version="@VERSION@">
+    <description>Read coverage calculator for metagenomics</description>
+    <macros>
+        <token name="@VERSION@">0.2.0.alpha7</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">coverm</requirement>
+    </requirements>
+    <version_command>coverm --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        coverm contigs
+        -t \${GALAXY_SLOTS}
+        --methods metabat
+        --bam-files $bam 
+        > depth.tsv
+    ]]></command>
+    
+    <inputs>
+        <param name="bam" type="data" format="bam" label="Input bam file" />
+    </inputs>
+
+    <outputs>
+        <data name="depth" format="json" label="{tool.name} on ${on_string} Depth" from_work_dir="depth.tsv"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    Documentation can be found at `<https://github.com/wwood/CoverM>`_.
+
+    ]]></help>
+</tool>