diff r_import_data.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_import_data.xml	Thu Feb 28 10:14:49 2019 -0500
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+<?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 name="FROGSSTAT Phyloseq Import Data" id="FROGSSTAT_Phyloseq_Import_Data" version="3.1">
+	<description>from 3 files: biomfile, samplefile, treefile </description>
+        <requirements>
+                <requirement type="package" version="3.1.0">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+	<command>r_import_data.py --biomfile $biomfile
+
+                                                      --samplefile $samplefile 
+                                                    #if $treefile
+                                                      --treefile $treefile 
+                                                    #end if
+                                                      --ranks "$ranks"
+	                                            #if $normalization
+                                                      --normalization
+                                                    #end if
+                                                      --html $html 
+                                                      --rdata $data
+	</command>
+    <inputs>
+		<!-- Files -->
+		<param format="biom1" name="biomfile" type="data" label="Standard biom file" help="The file contains the  OTU informations (format: biom1)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />
+        </param>
+        
+		<param format="tabular" name="samplefile" type="data" label="Sample tsv file" help="The file contains the samples informations (format: tabular)." optional="false">
+            <validator type="empty_field" message="This parameter is required." />                
+        </param>
+        
+		<param format="nhx" name="treefile" type="data" label="Tree file" help="The file contains the tree informations (format: Newick - nhx or nwk)." optional="true" />
+        
+        <!-- Parameters -->
+		<param name="ranks" type="text" label="Names of taxonomics levels" help="The ordered taxonomic levels stored in BIOM. Each level is separated by one space."  value="Kingdom Phylum Class Order Family Genus Species" size="80" optional="false"/>
+		<param name="normalization" type="boolean" label="Do you want to normalise your data ?" help="To normalise data before analysis." optional="false" /> 
+	</inputs>
+	<outputs>
+		<data format="rdata" name="data" label="${tool.name}: data.Rdata" from_work_dir="data.Rdata"/>
+		<data format="html" name="html" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="biomfile" value="input/chaillou.biom"/>
+			<param name="samplefile" value="input/sample_metadata.tsv"/>
+			<param name="treefile" value="input/tree.nwk"/>
+			<output name="data" value="references/14-phylo_import.Rdata" compare="sim_size" delta="10"/>
+		</test>
+	</tests>
+	<help>
+
+.. image:: static/images/frogs_images/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+.. class:: infomark page-header h2
+
+What it does
+
+Launch Rmarkdown script to import data from 3 files: biomfile, samplefile, treefile into a `phyloseq &lt;https://joey711.github.io/phyloseq/&gt;`_ object.
+
+.. class:: infomark page-header h2
+
+Inputs/Outputs
+
+.. class:: h3
+
+Input
+
+**OTU biom file**:
+
+The OTU biom file (format `biom1 &lt;http://biom-format.org/documentation/format_versions/biom-1.0.html&gt;`_).
+This file is the result of FROGS BIOM to std BIOM.
+The example of biom file: 
+
+  .. image:: static/images/frogs_images/biomfile.png 
+     :height: 30
+     :width: 733 
+
+**Newick file** (tree.nwk):
+
+Newick file (format `nxh &lt;https://en.wikipedia.org/wiki/Newick_format&gt;`_) is the result of FROGS Tree:
+
+  .. image:: static/images/frogs_images/nwk_treefile.png
+
+**Sample file**:
+The file contains the conditions of experiment with sample ID in the first column:
+  
+  .. image:: static/images/frogs_images/phyloseq_samplefile.png 
+     :height: 115
+     :width: 369
+      
+.. class:: h3
+
+Output
+
+**Html file** (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_): The summary of phyloseq object.
+  
+  .. image:: static/images/frogs_images/phyloseq_import_data_html.png 
+ 
+**Data file** (format rdata): The informations of data in one phyloseq object.
+
+
+.. 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>