--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_metaphlan2_output.xml	Wed Apr 20 07:52:41 2016 -0400
@@ -0,0 +1,67 @@
+<tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.1.0">
+    <description>output to extract abundance at different taxonomic levels</description>
+
+    <requirements>
+    </requirements>
+
+    <stdio>
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        python $__tool_directory__/format_metaphlan2_output.py
+            --metaphlan2_output $input_file
+            --all_taxo_level_abundance_file $all_taxo_level_abundance_file
+            --kingdom_abundance_file $kingdom_abundance_file
+            --phylum_abundance_file $phylum_abundance_file
+            --class_abundance_file $class_abundance_file
+            --order_abundance_file $order_abundance_file
+            --family_abundance_file $family_abundance_file
+            --genus_abundance_file $genus_abundance_file
+            --species_abundance_file $species_abundance_file
+            --strains_abundance_file $strains_abundance_file
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/>
+    </inputs>
+
+    <outputs>
+        <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" />
+        <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" />
+        <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" />
+        <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" />
+        <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" />
+        <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" />
+        <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" />
+        <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" />
+        <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="metaphlan2_output.txt"/>
+            <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/>
+            <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/>
+            <output name="phylum_abundance_file" file="phylum_abundance.txt"/>
+            <output name="class_abundance_file" file="class_abundance.txt"/>
+            <output name="order_abundance_file" file="order_abundance.txt"/>
+            <output name="family_abundance_file" file="family_abundance.txt"/>
+            <output name="genus_abundance_file" file="genus_abundance.txt"/>
+            <output name="species_abundance_file" file="species_abundance.txt"/>
+            <output name="strains_abundance_file" file="strains_abundance.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).
+
+9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances.
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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