diff normalisation.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/normalisation.xml	Thu Oct 25 05:01:13 2018 -0400
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+<?xml version="1.0"?>
+<!--
+# Copyright (C) 2015 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_normalisation" name="FROGS Abundance normalisation" version="2.0.0">
+        <description>Normalize OTUs abundance.</description>
+        <requirements>
+                <requirement type="package" version="2.0.1">frogs</requirement>
+        </requirements>
+        <!--stdio>
+                <exit_code range="1:" />
+                <exit_code range=":-1" />
+        </stdio-->
+	<command>
+		normalisation.py 
+		                       --input-biom $input_biom
+		                       --input-fasta $input_fasta
+		                       --num-reads $num_reads
+		                       --output-biom $output_biom
+		                       --output-fasta $output_fasta 
+		                       --summary-file $summary_file 
+	</command>
+	<inputs>
+		<param format="fasta" name="input_fasta" type="data" label="Sequence file" help="Sequence file to normalize (format: fasta)." />
+		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalize (format: BIOM)." />
+		<param name="num_reads" type="integer" optional="false" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
+	</inputs>
+	<outputs>
+		<data format="fasta" name="output_fasta" label="${tool.name}: normalized.fasta" from_work_dir="normalized.fasta" />
+		<data format="biom1" name="output_biom" label="${tool.name}: normalized.biom" from_work_dir="normalized.biom" />
+		<data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
+	</outputs>
+        <tests>
+                <test>
+	                <param name="input_fasta" value="references/04-filters.fasta"/>
+        	        <param name="input_biom" value="references/04-affiliation.biom"/>
+                	<param name="num_reads" value="100"/>
+	                <output name="summary_file" file="references/normalisation_report.html" compare="sim_size" delta="0" />
+                </test>
+        </tests>
+	<help>
+
+.. image:: static/images/FROGS_logo.png 
+   :height: 144
+   :width: 110
+
+
+.. class:: infomark page-header h2
+
+What it does
+
+This tool keeps, in each sample, the same number of elements by random sampling.
+
+.. class:: infomark page-header h2
+
+Inputs/outputs
+
+.. class:: h3
+
+Inputs
+
+**Sequence file**:
+
+The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file**:
+ 
+The abundance of each OTU in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (normalised_seed.fasta):
+
+ The normalised sequences file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file** (normalised_abundance.biom):
+
+ The normalised abundance file (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Summary file** (report.html):
+
+ Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+
+
+.. class:: infomark page-header h2
+
+Advices
+
+The number specified in "Number of reads" must be smaller than each total number of sequences by sample.
+
+
+----
+
+**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>