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+++ b/metaphlan2.xml	Thu Dec 17 04:03:29 2015 -0500
@@ -0,0 +1,218 @@
+<tool id="metaphlan_2" name="MetaPhlAn2" version="0.1.0">
+
+    <description>to profile the composition of microbial communities</description>
+
+    <requirements>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
+        <requirement type="package" version="2.0">metaphlan2</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal"   description="" />
+        <regex match="ERROR"
+               source="stderr"
+               level="fatal"
+               description="" />
+        <regex match="WARNING"
+               source="stderr"
+               level="warning"
+               description="" />
+    </stdio>
+
+    <version_command>
+<![CDATA[
+python \${METAPHLAN2_DIR}/metaphlan2.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[        
+        (which bowtie2 || exit 200)
+
+        &&
+
+        python \${METAPHLAN2_DIR}/metaphlan2.py
+            $input_file
+            -o $output_file
+
+            --input_type ${input_file.datatype.file_ext}
+            --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl 
+
+            --bowtie2_exe `which bowtie2`
+            --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
+
+            --no_map
+
+            -t $analysis_type.analysis_type_select
+            #if $analysis_type.analysis_type_select == "rel_ab"
+                --tax_lev $analysis_type.taxonomic_level 
+            #else if $analysis_type.analysis_type_select == "marker_ab_table"
+                --nreads $analysis_type.nreads
+            #else if $analysis_type.analysis_type_select == "marker_pres_table"
+                --pres_th $analysis_type.pres_th 
+            #end if
+
+            --min_cu_len $min_cu_len
+            --min_alignment_len $min_alignment_len
+
+            $ignore_viruses
+            $ignore_eukaryotes
+            $ignore_bacteria
+            $ignore_archaea
+
+            --stat_q $stat_q
+
+            #if $sam_output
+                -s $sam_output_file
+            #end if
+
+            #if $biom_output
+                --biom $biom_output_file
+            #end if
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
+
+        <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="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</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>
+            <when value="rel_ab">
+              <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
+                <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>
+            <when value="rel_ab_w_read_stats"/>
+            <when value="reads_map"/>
+            <when value="clade_profiles"/>
+            <when value="marker_ab_table">
+                <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
+            </when>
+            <when value="marker_pres_table">
+                <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
+            </when>
+        </conditional>
+
+        <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
+
+        <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
+
+        <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
+        <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
+        <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
+        <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
+
+        <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
+
+        <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
+        <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output_file" 
+            metadata="input_sequence_file" 
+            label="Profile of communities on ${on_string} (MetaPhlAn)" />
+
+        <data format="sam" name="sam_output_file" 
+            metadata="input_sequence_file" 
+            label="Sam output on ${on_string} (MetaPhlAn)">
+            <filter>sam_output</filter>
+        </data>
+        <data format="biom" name="biom_output_file" 
+            metadata="input_sequence_file" 
+            label="Biom output on ${on_string} (MetaPhlAn)">
+            <filter>biom_output</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="metaphlan2_input_sequences.fastq"/>
+            <param name="analysis_type_select" value="rel_ab" />
+            <param name="taxonomic_level" value="a" />
+            <param name="min_cu_len" value="2000" />
+            <param name="min_alignment_len" value="0" />
+            <param name="ignore_viruses" value="" />
+            <param name="ignore_eukaryotes" value="" />
+            <param name="ignore_bacteria" value="" />
+            <param name="ignore_archaea" value="" />
+            <param name="stat_q" value="0.1" />
+            <param name="sam_output" value='false' />
+            <param name="biom_output" value='true' />
+            <output name="output_file" file="metaphlan2_profiled_metagenome.txt"/>
+            <output name="biom_output_file" file="metaphlan2_biom.biom"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+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. For more information, check the 
+`user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
+
+-----
+
+**Input**
+
+Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
+SAM file or an intermediary mapping file of the metagenome generated by a 
+previous MetaPhlAn
+
+-----
+
+**Parameters**
+
+Several parameters can modulate the MetaPhlAn execution
+
+    * Mapping arguments
+
+        * Test to avoid saving the output of BowTie2
+
+    * Post-mapping arguments
+
+        * Taxonomic level for the relative abundance output
+        * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
+        * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
+        * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
+        * Quantile value
+
+    * Additional analysis types and arguments
+
+        * Type of analyse to perform and some parameters for specific analysis type
+
+-----
+
+**Outputs**
+
+The main output file is a tab-separated output file of the predicted taxon 
+relative abundances.
+
+Given the choosen parameters, other output files can be:
+
+    * a sam output file
+    * a biom output fime
+    * a BowTie2 output file
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1038/nmeth.3589</citation>
+    </citations>
+</tool>
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