# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1349890551 18000
# Node ID 61f300dbc6ac8df19c52efa6e467ca0855ef2fe7
# Parent  3468e70d3ed01de9dd7bd1203734ab995caedca7
Enable fastq input

diff -r 3468e70d3ed0 -r 61f300dbc6ac metaphlan.xml
--- a/metaphlan.xml	Wed Oct 10 08:49:28 2012 -0500
+++ b/metaphlan.xml	Wed Oct 10 12:35:51 2012 -0500
@@ -4,8 +4,8 @@
     <requirement type="package">bowtie2</requirement>
   </requirements>
   <description>Metagenomic Phylogenetic Analysis</description>
-  <command>
-	  metaphlan.py 
+  <command interpreter="python">
+	  \${METAPHLAN_PATH}/metaphlan.py 
 	  $input  
 	  --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa  
 	  --no_map  
@@ -14,9 +14,10 @@
   </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>