--- a/metaphlan.xml	Thu Oct 11 12:01:20 2012 -0500
+++ b/metaphlan.xml	Sun Dec 23 18:46:23 2012 +0100
@@ -5,40 +5,57 @@
   </requirements>
   <description>Metagenomic Phylogenetic Analysis</description>
   <command>
-	  python \${METAPHLAN_PATH}/metaphlan.py 
-	  $input  
-	  --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa  
-	  --no_map  
-	  -o $output  
-	  --bt2_ps $PresetsForBowtie2 
+    python \${METAPHLAN_PATH}/metaphlan.py 
+    $input 
+    -t $analysis_type.analysis_type_select 
+    #if $analysis_type.analysis_type_select == "rel_ab"
+    --tax_lev $analysis_type.taxonomic_level 
+    #end if
+    --bowtie2db \${METAPHLAN_PATH}/bowtie2db/mpa 
+    --no_map 
+    --bt2_ps $PresetsForBowtie2 
+    -o $output 
   </command>
-
   <inputs>
-	<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>
- 
-<tests>
-</tests>
-
-<help>
-
+    <param name="input" type="data" format="fasta,fastq" label="Input metagenome (multi-fasta of metagenomic reads, loaded with the Get Data module, see below for an example)"></param>
+    <conditional name="analysis_type">
+      <param name="analysis_type_select" type="select" label="Type of analysis to perform">
+        <option value="rel_ab" selected="true">profiling a metagenomes in terms of relative abundances</option>
+        <option value="reads_map">mapping from reads to clades (only reads hitting a marker)</option>
+        <option value="clade_profiles">normalized marker counts for clades with at least a non-null marker</option>
+      </param>
+      <when value="rel_ab">
+        <param name="taxonomic_level" type="select" label="Taxonomic level">
+          <option value="a" selected="true">all taxonomic levels</option>
+          <option value="k">kingdoms (Bacteria and Archaea) only</option>
+          <option value="p">phyla only</option>
+          <option value="c">classes only</option>
+          <option value="o">orders only</option>
+          <option value="f">families only</option>
+          <option value="g">genera only</option>
+          <option value="s">species only</option>
+        </param>
+      </when>
+    </conditional>
+    <param name="PresetsForBowtie2" type="select" label="Sensitivity options for read-marker similarity (as described by BowTie2)" help="Sensitive Local is recommended for avoiding overly-sensitive hits when using non-preprocessed fastq files">
+      <option value="very-sensitive-local" selected="true">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 name="output" format="tabular" label="${tool.name} on ${on_string} (${analysis_type.analysis_type_select} analysis)"/>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
 .. class:: infomark
 
-**Input example:** You can try out MetaPhlAn using the synthetic dataset (250,000 reads) available at: http://huttenhower.sph.harvard.edu/sites/default/files/LC1.fna . There is no need to download the file, you can just copy-and-paste the dataset address in the "Upload File" module inside the "Load Data" link here in the left panel.
+**Input example:** You can try out MetaPhlAn using the synthetic dataset (250,000 reads) available at: http://huttenhower.sph.harvard.edu/sites/default/files/LC1.fna . There is no need to download the file, you can just copy-and-paste the dataset address in the "Upload File" module inside the "Get Data" link here in the left panel.
 
 .. class:: infomark
 
@@ -54,7 +71,7 @@
 
 MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from reference genomes, allowing orders of magnitude speedups and unambiguous taxonomic assignments.
 
-Although MetaPhlAn can use both BlastN and BowTie2 in the read-to-marker mapping step, this Galaxy module uses only BowTie2 for computational reasons. 
+Although MetaPhlAn can use both BlastN and BowTie2 in the read-to-marker mapping step, this Galaxy module uses only BowTie2 for computational reasons.
 
 For additional information about MetaPhlAn and the MetaPhlAn command line package, please refer to http://huttenhower.sph.harvard.edu/metaphlan or to the paper reported below. Please notice that most of the additional parameters that can be tuned with the command line version are set here to the default values.
 
@@ -62,15 +79,15 @@
 
 **Inputs**
 
-The input file must be a multi-fasta file containing metagenomic reads loaded with the "Get Data" module in the left panel. Reads can be as short as ~40 nt although lengths higher than 70 nt are recommended. 
+The input file must be a multi-fasta file containing metagenomic reads loaded with the "Get Data" module in the left panel. Reads can be as short as ~40 nt although lengths higher than 70 nt are recommended.
 
 A synthetic metagenome you can use as sample input is available at http://huttenhower.sph.harvard.edu/sites/default/files/LC1.fna
 
 **Outputs**
 
-The output is a two column tab-separated plain file reporting the predicted microbial clades present in the metagenomic samples and the corresponding relative abundances. 
+The output is a two column tab-separated plain file reporting the predicted microbial clades present in the metagenomic samples and the corresponding relative abundances.
 
-All taxonomic levels from domain to species will be reported and higher taxonomic levelis contain the sum of the abundances of its taxonomic leaf nodes (usually species) and, possibly, some lower level "unclassified" clades. 
+All taxonomic levels from domain to species will be reported and higher taxonomic levelis contain the sum of the abundances of its taxonomic leaf nodes (usually species) and, possibly, some lower level "unclassified" clades.
 
 -----
 
@@ -79,17 +96,15 @@
 If you find MetaPhlAn useful in your research, please cite our paper:
 
 | `Nicola Segata`_, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, `Curtis Huttenhower`_.
-| **"Fast and accurate metagenomic profiling of microbial community composition using unique clade-specific marker genes"**
-| Nature Methods, 2012 (in press)
+| "`Metagenomic microbial community profiling using unique clade-specific marker genes`_"
+| Nature Methods 9(8), 811-814 (2012)
 
 .. _Nicola Segata: nsegata@hsph.harvard.edu
 .. _Curtis Huttenhower: chuttenh@hsph.harvard.edu
+.. _Metagenomic microbial community profiling using unique clade-specific marker genes: http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2066.html
 
-If you have any questions or comments, feel free to `contact  us`_. Additional information are available at http://huttenhower.sph.harvard.edu/metaphlan and in the FAQ at the same page. You can also join and use our user group at https://groups.google.com/d/forum/metaphlan-users
+If you have any questions or comments, feel free to `contact us`_. Additional information are available at http://huttenhower.sph.harvard.edu/metaphlan and in the FAQ at the same page. You can also join and use our user group at https://groups.google.com/d/forum/metaphlan-users
 
 .. _contact us: nsegata@hsph.harvard.edu
-
-
-    </help>
+  </help>
 </tool>
-

--- a/metaphlan_to_phyloxml.xml	Thu Oct 11 12:01:20 2012 -0500
+++ b/metaphlan_to_phyloxml.xml	Sun Dec 23 18:46:23 2012 +0100
@@ -1,17 +1,15 @@
 <tool id="meta_to_phylo" name="MetaPhlAn to PhyloXML" version="1.0.0">
- <description>Converter</description>
- <command interpreter="python">
-metaphlan_to_phyloxml.py $input $output
- </command>
- <inputs>
-  <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
- </inputs>
- <outputs>
+  <description>converter</description>
+  <command interpreter="python">metaphlan_to_phyloxml.py $input $output</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="MetaPhlAn relative abundances"/>
+  </inputs>
+  <outputs>
     <data format="xml" name="output" label="${tool.name} on ${on_string}" /> 
- </outputs>
- <tests>
- </tests>
- <help>
-  MetaPhlAn to PhyloXML Converter
- </help>
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+This tool converts the results of metagonome profiling performed with MetaPhlAn from tabular to PhyloXML format. The tool accepts as input only the result of rel_ab analysis (profiling in terms of relative abundaces), not reads_map or clade_profiles analysis.
+  </help>
 </tool>

--- a/tool_dependencies.xml	Thu Oct 11 12:01:20 2012 -0500
+++ b/tool_dependencies.xml	Sun Dec 23 18:46:23 2012 +0100
@@ -3,7 +3,7 @@
     <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="shell_command">hg clone https://bitbucket.org/nsegata/metaphlan</action>
                 <action type="move_directory_files">
                     <source_directory>.</source_directory>
                     <destination_directory>$INSTALL_DIR</destination_directory>