diff tree.xml @ 0:59bc96331073 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tree.xml	Thu Feb 28 10:14:49 2019 -0500
@@ -0,0 +1,126 @@
+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2017 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_Tree" name="FROGS Tree" version="3.1">
+	<description>Reconstruction of phylogenetic tree </description>
+ 	<requirements>
+                <requirement type="package" version="3.1.0">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+	<command>tree.py 
+                                            --input-otu $input_otu
+                                            --biomfile $biomfile
+                                            --nb-cpus \${GALAXY_SLOTS:-1}
+                                            --out-tree $out_tree
+                                            --html $html
+	</command>
+    <inputs>
+	<!-- Files -->
+	<param format="fasta" name="input_otu" type="data" label="OTUs sequence file" help="OTUs sequence file (format: fasta). Warning: FROGS Tree does not work on more than 10000 sequences!" optional="false">
+        	<validator type="empty_field" message="This parameter is required." />
+        </param>
+        <param format="biom1" name="biomfile" type="data" label="Biom file" help="The abundance table of OTUs (format: biom)." optional="false">
+        	<validator type="empty_field" message="This parameter is required." />
+        </param>
+    </inputs>
+	<outputs>
+		<data format="nhx" name="out_tree" label="${tool.name}: tree.nwk" from_work_dir="tree.nwk"/>
+        	<data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="input_otu" value="references/04-filters.fasta"/>
+			<param name="biomfile" value="references/06-affiliation.biom"/>
+			<!--output name="out_tree" value="references/13-tree-mafft.nwk"/-->
+			<!--output name="html" value="references/13-tree-mafft.html"/-->
+			<output name="html">
+ 		        	<assert_contents>
+                    		<has_text_matching expression="FROGS\sTree" />
+                    		<has_text_matching expression="abundance_removed.*:\s0" />
+                    		<has_text_matching expression="abundance_kept.*:\s45574" />
+                    		<has_text_matching expression="otu_removed.*:\s0" />
+                    		<has_text_matching expression="otu_kept.*:\s86" />
+                		</assert_contents>
+			</output>
+		</test>
+	</tests>
+	<help>
+.. image:: static/images/frogs_images/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Creation of a multiple alignment of OTUs with `Mafft &lt;http://mafft.cbrc.jp/alignment/software&gt;`_.
+And creation of a rooted phylogenetic tree with `FastTree &lt;http://www.microbesonline.org/fasttree/&gt;`_ and `Phangorn R package &lt;https://cran.r-project.org/web/packages/phangorn/index.html&gt;`_.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTUs fasta file**:
+
+The OTUs sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+Careful: FROGS Tree works only with less than 10 000 sequences!
+ 
+ .. image:: static/images/frogs_images/frogs_tree_otufile.png
+     
+**OTUs biom file**:
+
+The OTUs biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
+This file can be obtained in particular with the FROGS pipeline.
+
+.. class:: h3
+
+Outputs
+
+**Newick file** (tree.nwk):
+
+The phylogenetic tree in Newick format (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
+
+ .. image:: static/images/frogs_images/nwk_treefile.png
+
+**Html file** (summary.html):
+   
+The summary file describing which OTUs are contained or not in the phylogenetic tree.
+
+.. class:: infomark page-header h2
+   
+**Contact**
+
+Contacts: [e-mail]
+
+Repository: https://github.com/geraldinepascal/FROGS
+website: http://frogs.toulouse.inra.fr/
+
+Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
+
+	</help>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btx791</citation>
+	</citations>
+
+</tool>