--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_to_stdBiom.xml	Thu Oct 25 05:01:13 2018 -0400
@@ -0,0 +1,107 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 INRA
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+-->
+<tool id="FROGS_biom_to_stdBiom" name="FROGS BIOM to std BIOM" version="1.1.0">
+	<description>Converts a FROGS BIOM in fully compatible BIOM.</description>
+ 	<requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+	<command>
+		biom_to_stdBiom.py 
+		                --input-biom $input_biom
+		                --output-biom $output_biom
+		                --output-metadata $output_metadata 
+	</command>
+	<inputs>
+		<!-- Files -->
+		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The FROGS BIOM file to convert (format: BIOM)." optional="false" />
+	</inputs>
+	<outputs>
+		<data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom"/>
+		<data format="tabular" name="output_metadata" label="${tool.name}: blast_metadata.tsv" from_work_dir="blast_metadata.tsv" />
+	</outputs>
+	<tests>
+		<test>
+			<param name="input_biom" value="references/04-affiliation.biom"/>
+			<output name="output_biom" value="references/08-affiliation_std.biom"/>
+			<output name="output_metadata" value="references/08-affiliation_multihit.tsv"/>
+		</test>
+	</tests>
+	<help>
+
+.. image:: static/images/FROGS_logo.png
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+Converts a BIOM generated by FROGS in generic BIOM.
+
+The detailed blast affiliations can trigger problem with tools like Qiime. This tool extracts the problematic metadata in a second file and writes a BIOM usable in every tools using BIOM.
+
+.. class:: h3
+
+Inputs
+
+**Abundance file**:
+ 
+The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Abundance file**:
+
+ The abundance without the incompatible metadata (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Blast metadata file**:
+
+ The details for each alignment on clusters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
+
+
+.. class:: infomark page-header h2
+
+How it works
+
+FROGS BIOM to std BIOM extracts the blast alignment metadata in a second file, write a BIOM usable in every tools using BIOM and defined the taxonomy provided by blast as main taxonomy.
+
+
+
+----
+
+**Contact**
+
+Contacts: frogs@inra.fr
+
+Repository: https://github.com/geraldinepascal/FROGS
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
+
+Depending on the help provided you can cite us in acknowledgements, references or both.
+	</help>
+	<citations>
+		<citation type="doi">10.7287/peerj.preprints.386v1</citation>
+	</citations>
+</tool>