# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1349974880 18000
# Node ID 80b22b31633fc233dca42d54240983f244323280
# Parent  e88fa24fa837ed913a58da7bb5597c0ee5ed98b3
Updated for MetaPhlAn v1.7 and tool_dependencies added for auto install

diff -r e88fa24fa837 -r 80b22b31633f metaphlan.xml
--- a/metaphlan.xml	Wed Jun 06 10:41:23 2012 -0400
+++ b/metaphlan.xml	Thu Oct 11 12:01:20 2012 -0500
@@ -1,28 +1,32 @@
-<tool id="metaphlan" name="MetaPhlAn" version="1.6.0">
-<requirements>
-<requirement type="package">metaphlan</requirement>
-<requirement type="package">bowtie2</requirement>
-</requirements>
+<tool id="metaphlan" name="MetaPhlAn" version="1.7.0">
+  <requirements>
+    <requirement type="package" version="1.7.0">metaphlan</requirement>
+    <requirement type="package">bowtie2</requirement>
+  </requirements>
   <description>Metagenomic Phylogenetic Analysis</description>
   <command>
-	  metaphlan.py 
+	  python \${METAPHLAN_PATH}/metaphlan.py 
 	  $input  
-	  --bowtie2db ${GALAXY_DATA_INDEX_DIR}/shared/metaphlan/bowtie2db/mpa  
+	  --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa  
 	  --no_map  
 	  -o $output  
 	  --bt2_ps $PresetsForBowtie2 
   </command>
 
   <inputs>
-	<param format="fasta" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
+	<param format="fasta,fastq" name="input" type="data" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
 	<param name="PresetsForBowtie2" type="select" format="text">
 		<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
+                <help>sensitive-local is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files</help>
 			<option value="very-sensitive-local">Very Sensitive  Local</option>
 			<option value="sensitive-local">Sensitive  Local</option>
 			<option value="very-sensitive">Very Sensitive</option>
 			<option value="sensitive">Sensitive</option>
 	</param>			
 </inputs>
+<stdio>
+    <exit_code range="1:"  level="fatal"   description="MetaPhlAn error" />
+</stdio>
 <outputs>
 	<data format="tabular" name="output" />
 </outputs>
diff -r e88fa24fa837 -r 80b22b31633f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 11 12:01:20 2012 -0500
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="metaphlan" version="1.7.0">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">hg clone http://bitbucket.org/nsegata/metaphlan</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="METAPHLAN_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+
+            </actions>
+        </install>
+        <readme>
+These links provide information for the metaphlan package:
+http://huttenhower.sph.harvard.edu/metaphlan
+https://groups.google.com/forum/#!forum/metaphlan-users
+        </readme>
+    </package>
+</tool_dependency>
+