<tool id="metaphlan2_hutlab" name="MetaPhlAn2" version="2.5.0">


	<description>metagenomic profiler V2</description>
	<command interpreter="python">metaphlan2.py $input 
		--mpa_pkl   $METAPHLAN_PATH/db_v20/mpa_v20_m200.pkl    
		--bowtie2db $METAPHLAN_PATH/db_v20/mpa_v20_m200 
		--input_type  fastq
		--no_map 
		--bt2_ps $PresetsForBowtie2  
		#if $str($gchoice_post_mapping.global_choice_post_mapping)  == "1":
			--tax_lev $gchoice_post_mapping.Taxonomic_Level
			--min_cu_len $gchoice_post_mapping.min_cu_len

			#if $str($gchoice_post_mapping.Ignore_Viruses)  == "1":
				--ignore_viruses
			#end if		
			#if $str($gchoice_post_mapping.Ignore_Eukaryotes)  == "1":
				--ignore_eukaryotes   
			#end if	
			#if $str($gchoice_post_mapping.Ignore_Bacteria)  == "1":
				--ignore_bacteria
			#end if	
			#if $str($gchoice_post_mapping.Ignore_Archaea)  == "1":
				--ignore_archaea
			#end if	

			--stat_q $gchoice_post_mapping.stat_q
		#end if
 
		#if $str($gchoice_additional_analysis_types.global_additional_analysis_types)  == "1":
 			-t $gchoice_additional_analysis_types.Analysis_Type 
			#if  int($gchoice_additional_analysis_types.nreads) > 0:
				--nreads $gchoice_additional_analysis_types.nreads
			#end if	
			
			#if  int($gchoice_additional_analysis_types.pres_th) > 0:
				--pres_th  $gchoice_additional_analysis_types.pres_th
			#end if	
			
			#if $str($gchoice_additional_analysis_types.clade)  != " ":
				--clade $gchoice_additional_analysis_types.clade 
				#if  int($gchoice_additional_analysis_types.min_ab) > 0:
						 --min_ab  $gchoice_additional_analysis_types.min_ab             
				#end if				
			#end if				
			
		#end if
 		-o $output 
		
			
		#if $str($gchoice_biom.global_biom)  == "1":
			--biom $biom_output
			--mdelim $gchoice_biom.MetadataDelimiterChar
		#end if	
	</command>
	<inputs>
		<param format="fastq" name="input" type="data" label="Input metagenome (fastq of metagenomic reads, loaded with the Get Data module )"></param>

		<param name="PresetsForBowtie2" type="select" format="text" >
			<label>Sensitivity options for read-marker similarity (as described by BowTie2)</label>
				<option value="very-sensitive">Very Sensitive</option>
				<option value="sensitive">Sensitive</option>
				<option value="very-sensitive-local">Very Sensitive  Local</option>
				<option value="sensitive-local">Sensitive  Local</option>

		</param>	
		
		
		
	<conditional name="gchoice_post_mapping">
        	<param name="global_choice_post_mapping" type="select" label="Display Post Mapping Advanced Parameters"  multiple="False" help="Select Post Mapping advanced choices ">
        		<option value="0" selected='True'>No</option>
				<option value="1">Yes</option>
        	</param>
           	<when value="0">
 				<param name="min_cu_len" type="hidden"  value=""  />
			</when>

        	<when value="1">
				<param name="Taxonomic_Level" type="select" value="a" format="text" >
					<label>Taxonomic Level</label>
						<option value="a">All taxonomic levels</option>
						<option value="k">Kingdoms (Bacteria and Archaea) only</option>
						<option value="p">Phyla 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>
				<param name="min_cu_len" type="integer" size="4"   value="2000" label="Minimum total nucleotide length for the markers in a clade "/>

				<param name="Ignore_Viruses" type="select" label="Profile viral organisms" value="0" >
						<option value="0">Yes</option>
						<option value="1">No</option>
				</param>
				
				<param name="Ignore_Eukaryotes" type="select" label="Profile eukaryotic organisms" value="0" >
						<option value="0">Yes</option>
						<option value="1">No</option>
				</param>		
				
				<param name="Ignore_Bacteria" type="select" label="Profile bacterial organisms" value="0" >
						<option value="0">Yes</option>
						<option value="1">No</option>
				</param>

				<param name="Ignore_Archaea" type="select" label="Profile archeal organisms" value="0" >
						<option value="0">Yes</option>
						<option value="1">No</option>
				</param>	

				<param name="stat_q" type="float"     value="0.1"  min="0" max="1.0" label=" Quantile value for the robust average "/>
				
			</when>
        </conditional>
		
	<conditional name="gchoice_additional_analysis_types">
        	<param name="global_additional_analysis_types" type="select" label="Display additional analysis types and arguments advanced parameters"  multiple="False" help="Select additional analysis types and argument advanced choices ">
        		<option value="0" selected='True'>No</option>
				<option value="1">Yes</option>
        	</param>
           	<when value="0">
 				<param name="Analysis_Type" type="hidden"  value=""  />
			</when>

        	<when value="1">
				<param name="Analysis_Type" type="select" value="rel_ab" format="text" >
					<label>Analysis Type: Type of Analysis to perform</label>
						<option value="rel_ab">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>
						<option value="marker_ab_table">normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
						<option value="marker_pres_table">list of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
				</param>
				
				<param name="nreads" type="integer" size="4"   value="0" label="The total number of reads in the original metagenome "/>
				<param name="pres_th" type="integer" size="4"  value="0"   label="Threshold for calling a marker present"/>
				<param name="clade" label="The clade for clade specific strain tracker analysis"  value=" " type="text" format="text"/>
				<param name="min_ab" type="integer" size="4"  value="0" min="0" max="100"  label="The minimum percentage abundance for the clade in the clade specific strain tracker analysis"/>	
	
			</when>
        </conditional>
		
		
		
		
		<conditional name="gchoice_biom">
        	<param name="global_biom" type="select" label="Display additional biom advanced parameters"  help="Select additional biom  choices ">
        		<option value="0" selected='True'>No</option>
				<option value="1">Yes</option>
        	</param>
           	<when value="0">
			</when>

        	<when value="1">
				<param name="MetadataDelimiterChar" label="Delimiter for bug metadata if biom file requested - defaults to pipe. e.g. the pipe in k__Bacteria|p__Proteobacteria"  value="|" type="text" format="text"/>
			</when>
        </conditional>
 

	</inputs>
	<outputs>
		<data name="output" format="tabular" />
        <data name="biom_output"  format="text">
            <filter>gchoice_biom["global_biom"] == "1"</filter>
        </data>
	 

	</outputs>
  <requirements>
    <requirement type="set_environment">METAPHLAN2_PATH</requirement>
  </requirements>  
  <help>
**MetaPhlAn**  is a computational tool for profiling the composition of microbial communities *(Bacteria, Archaea, Eukaryotes and Viruses)* from metagenomic shotgun sequencing data with species level resolution. 

From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:

* Unambiguous taxonomic assignments 

* Accurate estimation of organismal relative abundance 

* Species-level resolution for bacteria, archaea, eukaryotes and viruses 

* Strain identification and tracking

* Orders of magnitude speedups compared to existing methods.

EXAMPLE
-------

Here is an infographic of the application of the Human Microbiome Project results obtained applying MetaPhlAn on the 690 shotgun sequencing samples.  The image has been produced with GraPhlAn.


.. image::    https://bytebucket.org/nsegata/metaphlan/wiki/hmptree13_nl_bb.png
    :height: 500
    :width: 600



If you use this software, please cite :
=======================================

**Metagenomic microbial community profiling using unique clade-specific marker genes.** Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower. Nature Methods, 8, 811–814, 2012

  </help>
</tool>