diff r_alpha_diversity.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/r_alpha_diversity.xml	Thu Feb 28 10:14:49 2019 -0500
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+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+# 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 name="FROGSSTAT Phyloseq Alpha Diversity" id="FROGSSTAT_Phyloseq_Alpha_Diversity" version="3.1">
+	<description>with richness plot</description>
+        <requirements>
+                <requirement type="package" version="3.1.0">frogs</requirement>
+        </requirements>
+	<stdio>
+		<exit_code range="1:" />
+		<exit_code range=":-1" />
+	</stdio>
+	<command>r_alpha_diversity.py
+                                             --rdata $data 
+                                             --varExp $varExp
+                                             --alpha-measures $measures
+                                             --alpha-out $alphaD 
+                                             --html $html
+	</command>
+    <inputs>
+		<!-- Files -->
+	    <param format="rdata" name="data" type="data" label="Phyloseq object (format rdata)" help="This file is the result of FROGS Phyloseq Import Data tool." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+		<!-- Parameters -->	
+		<param name="varExp" type="text" label="Experiment variable" help="The experiment variable that you want to analyse." optional="false" value="" size="40">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>        
+	    <param name="measures" type="select" label="The alpha diversity indices to compute" multiple="true" display="checkboxes">
+             <option value="Observed" selected="True">Observed</option>
+             <option value="Chao1" selected="True">Chao1</option>
+             <option value="Shannon" selected="True">Shannon</option>
+             <option value="InvSimpson" selected="True">InvSimpson</option>
+             <option value="Simpson">Simpson</option>
+             <option value="ACE">ACE</option>
+             <option value="Fisher">Fisher</option>
+        </param>
+	</inputs>
+	<outputs>
+		<data format="tabular" name="alphaD" label="${tool.name}: alpha_diversity.tsv" from_work_dir="alpha_diversity.tsv"/>
+		<data format="html" name="html" label="${tool.name}: alpha_diversity.html" from_work_dir="alpha_diversity.html"/>
+	</outputs>
+        <tests>
+            <test>
+                <param name="data" value="references/14-phylo_import.Rdata" />
+                <param name="varExp" value="EnvType" />
+                <param name="measures" value="Observed,Chao1,Shannon" />
+                <output name="alphaD" file="references/16-phylo_alpha_div.tsv" compare="diff" lines_diff="0" />
+            </test>
+        </tests>
+<help>
+		
+.. image:: static/images/frogs_images/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Using `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ and customized R function, this tool constructs richness plots to visualise sample alpha diversity.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**Data file** (format RData):
+One phyloseq object containing OTU abundance table, their taxonomies (and optionnaly a phylogenetics tree, and the sample experiment metadata.
+This file is the result of "FROGS Phyloseq Import Data tool".
+
+.. class:: h3
+
+Output
+
+**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): the review of richness plots and rarefaction curves.
+
+.. image:: static/images/frogs_images/phyloseq_plot_richness.png 
+     :height: 400
+     :width: 525 
+
+.. image:: static/images/frogs_images/phyloseq_plot_richness_box.png
+     :height: 400
+     :width: 499
+     
+.. image:: static/images/frogs_images/phyloseq_rarefaction_curves.png
+     :height: 400
+     :width: 498
+
+**Alpha diversity table** (alpha_diversity.tsv):
+The data file containing table of alpha diversity indices.
+
+.. image:: static/images/frogs_images/phyloseq_alpha_diversity_table.png
+
+.. 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>