diff r_import_data.xml @ 0:76c750c5f0d1 draft default tip

planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_import_data.xml	Thu Oct 25 05:01:13 2018 -0400
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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="1.0.0">
+	<description>from 3 files: biomfile, samplefile, treefile </description>
+ 	<requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio>
+	<command>r_import_data.py --biomfile $biomfile
+                                                   #if $samplefile
+                                                      --samplefile $samplefile 
+                                                   #end if
+                                                      --treefile $treefile 
+                                                      --ranks "$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="references/chaillou.biom"/>
+			<param name="samplefile" value="references/sample_metadata.tsv"/>
+			<param name="treefile" value="references/tree.nwk"/>
+			<output name="data" value="references/11-phylo_import.Rdata"/>
+		</test>
+	</tests>
+
+	<help>
+
+.. image:: static/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/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/nwk_treefile.png
+
+**Sample file**:
+The file contains the conditions of experiment with sample ID in the first column:
+  
+  .. image:: static/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/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
+
+Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Combes S., Hernandez-Raquet G., Pascal G., 2016. FROGS: Find Rapidly OTU with Galaxy Solution. In: ISME-2016 Montreal, CANADA ,* http://bioinfo.genotoul.fr/wp-content/uploads/FROGS_ISME2016_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>