--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2.xml	Wed Jun 01 10:45:26 2016 -0400
@@ -0,0 +1,213 @@
+<tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0">
+
+    <description>to profile the composition of microbial communities</description>
+
+    <macros>
+        <import>metaphlan2_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <version_command>
+<![CDATA[
+metaphlan2.py -v
+]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        (which bowtie2 || exit 200)
+
+        &&
+
+        #if $db.db_selector == "history"
+            mkdir ref_db
+            &&
+            bowtie2-build $db.db_sequences ref_db/ref_db
+            &&
+            python $__tool_directory__/transform_json_to_pkl.py
+                --json_input $db_metadata
+                --pkl_output ref_db/metadata.pkl
+            &&
+        #end if
+
+        metaphlan2.py
+            $input_file
+            -o $output_file
+            --input_type ${input_file.datatype.file_ext}
+
+            --bowtie2_exe `which bowtie2`
+
+            #if $db.db_selector == "cached"
+                #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
+                #set $db_choice = $db.cached_db.value
+                --bowtie2db $table[$db_choice]
+                --mpa_pkl $table[$db_choice]".pkl"
+            #else
+                --bowtie2db ref_db/ref_db
+                --mpa_pkl ref_db/metadata.pkl
+            #end if
+
+            --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
+            -s $sam_output_file
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/>
+
+        <conditional name="db">
+            <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
+                <option value="cached" selected="true">Locally cached</option>
+                <option value="history">From history</option>
+            </param>
+
+            <when value="cached">
+                <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
+                <options from_data_table="metaphlan2_db" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/>
+                <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/>
+            </when>
+        </conditional>
+
+        <conditional name="analysis_type">
+            <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)">
+              <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>
+              <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_counts">Non-normalized marker counts (use with extreme caution)</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" help="(--tax_lev)">
+                <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="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_counts"/>
+
+            <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=""/>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
+        <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: Sam file" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="input_sequences.fasta"/>
+            <param name="db_selector" value="history" />
+            <param name="db_metadata" value="marker_metadata.json" />
+            <param name="db_sequences" value="marker_sequences.fasta" />
+            <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" />
+            <output name="output_file" file="community_profile.tabular"/>
+        </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/>`_.
+
+**Inputs**
+
+Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.
+
+It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:
+
+::
+
+  {
+    "taxonomy": {
+            "taxonomy of genome1": genome1_length,
+            "taxonomy of genome2": genome2_length,
+            ...
+        }
+    "markers": {
+            "marker1_name": {
+                "clade": the clade that the marker belongs to,
+                "ext": [list of external genomes where the marker appears],
+                "len": length of the marker,
+                "score": score of the marker,
+                "taxon": the taxon of the marker
+            }
+            ...
+        }
+  }
+
+The marker names correspond to sequence name in corresponding fasta file with marker gene sequences.
+
+**Outputs**
+
+The main output file is a tab-separated output file of the predicted taxon relative abundances.
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1038/nmeth.3589</citation>
+    </citations>
+</tool>