diff tree.xml @ 0:27f57425dc55 draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.2.1 commit 30428631e20fff407dde4d0026d28d3fd0875811"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tree.xml	Wed Mar 03 17:03:54 2021 +0000
@@ -0,0 +1,129 @@
+<?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="3.2.1">
+    <description>Reconstruction of phylogenetic tree </description>
+    <requirements>
+        <requirement type="package" version="3.2.1">frogs</requirement>
+        <requirement type="package" version="7.407">mafft</requirement>
+        <requirement type="package" version="2.1.09">fasttree</requirement>
+        <requirement type="package" version="3.6.3">r-base</requirement>
+        <requirement type="package" version="2.5.5">r-phangorn</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command>
+        tree.py 
+            --input-sequences $input_otu
+            --biom-file $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/09-normalisation.fasta"/>
+            <param name="biomfile" value="references/09-normalisation.biom"/>
+            <output name="out_tree" value="references/15-tree-mafft.nwk" compare="sim_size" delta="30"/>
+            <output name="html" value="references/15-tree-mafft.html" compare="diff" lines_diff="2"/>
+            <output name="html" value="references/15-tree-mafft.html" compare="sim_size" delta="30"/>
+            <output name="html">
+                 <assert_contents>
+                    <has_text_matching expression="FROGS\sTree" />
+                    <has_text_matching expression="abundance_removed.*:\s0" />
+                    <has_text_matching expression="abundance_kept.*:\s300" />
+                    <has_text_matching expression="otu_removed.*:\s0" />
+                    <has_text_matching expression="otu_kept.*:\s50" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+.. image:: static/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_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 `nwk or nhx &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_).
+
+ .. image:: static/images/FROGS_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]
+
+Repositories: https://github.com/geraldinepascal/FROGS, https://github.com/geraldinepascal/FROGS-wrappers
+
+Website: http://frogs.toulouse.inrae.fr/
+
+Please cite the **FROGS article**: `Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution. &lt;https://doi.org/10.1093/bioinformatics/btx791&gt;`_
+
+    </help>
+</tool>