# HG changeset patch
# User chrisd
# Date 1476011181 14400
# Node ID 6e3417efcef347af0139505885cfd2012ca20dbd

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/resistomeanalyzer commit e5dfdf9aa83af409ee99a0259ceb23b305b8f949-dirty

diff -r 000000000000 -r 6e3417efcef3 resistome_analyzer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resistome_analyzer.xml	Sun Oct 09 07:06:21 2016 -0400
@@ -0,0 +1,32 @@
+<tool id="resistome_analyzer" name="ResistomeAnalyzer" version="0.1.0">
+    <description>A simple tool for analyzing the resistome of metagenomic sequence data</description>
+    <requirements>
+	<requirement type="package" version="0.1">resistomeanalyzer</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	resistome
+	  -ref_fp $reference
+	  -annot_fp $annotation
+	  -sam_fp $sam
+	  -gene_fp $gene
+	  -mech_fp $mech
+	  -class_fp $class
+	  -group_fp $group
+    ]]></command>
+    <inputs>
+	<param type="data" name="reference" format="fasta" label="Reference sequence" />
+	<param type="data" name="sam" format="sam" label="SAM file" />
+	<param type="data" name="annotation" format="csv" label="Annotation file" />
+    </inputs>
+    <outputs>
+	<data name="gene" format="tabular" />
+	<data name="mech" format="tabular" />
+	<data name="class" format="tabular" />
+	<data name="group" format="tabular" />
+    </outputs>
+    <citations>
+    </citations>
+</tool>
diff -r 000000000000 -r 6e3417efcef3 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Oct 09 07:06:21 2016 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="resistomeanalyzer" version="0.1">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone --recursive https://github.com/cdeanj/resistomeanalyzer.git</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>resistome</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling resistome_analyzer requires a C++ compiler</readme>
+    </package>
+</tool_dependency>