diff normalisation.xml.bak @ 30:fce825ec2c84 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 01b92e7e17eb8bc125451bf41684f512cf16d3c5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalisation.xml.bak	Fri May 02 07:44:22 2025 +0000
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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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+        <description>Normalise ASV abundance. </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+
+	<command detect_errors="exit_code">
+		[<![CDATA[ 
+		normalisation.py 
+			--input-biom '$input_biom'
+			--input-fasta '$input_fasta'
+
+			#if $sampling_method.sampling_by_min == "yes"
+				--sampling-by-min
+			#else
+				--num-reads '$sampling_method.num_reads'
+
+				#if $sampling_method.delete_samples == "true"
+				--delete-samples
+				#end if
+			#end if
+
+			--output-biom '$output_biom'
+			--output-fasta '$output_fasta'
+			--summary-file '$summary_file'
+		]]>					
+	</command>
+	<inputs>
+		<param format="fasta" argument="--input-fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." />
+		<param format="biom1" argument="--input-biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." />
+		<conditional name="sampling_method">
+			<param argument="--sampling-by-min" type="select" label="Sampling method" help="Sampling by the number of sequences of the smallest sample, or select a number manually" display="radio">
+            	<option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option>
+            	<option value="no">Select a number of sequences</option>
+			</param>
+		<when value="yes"/>
+		<when value="no">
+			<param argument="--num-reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." />
+			<param argument="--delete-samples" type="select" label="Remove samples that have an initial number of reads below the number of reads to sample ?" display="radio">
+                <option value="false">No, subsampling threshold need to at most equal to the smallest sample</option>
+            	<option value="true">Yes, subsampling threshold may be greater than the smallest sample</option>
+            </param>
+		</when>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
+		<data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.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/08-affiliation_postprocessed.fasta"/>
+	        <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/>
+        	<conditional name="sampling_method">
+        	<param name="sampling_by_min" value="no"/>
+        	<param name="num_reads" value="100"/>
+        	</conditional>
+            <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" />
+            <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" />
+            <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" />
+        </test>
+    </tests>
+	<help>
+
+@HELP_LOGO@
+
+.. 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 ASV in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Sampling method**:
+
+Sequence normalisation method :
+
+ - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of sequences of the smallest sample, and selects this number for all other samples.
+ - **Select number of sequences** : Manually select a number of sequences.
+
+With this number, a random draw of sequences is made and once normalisation is complete, each sample will contain the specified number of sequences.
+
+.. class:: warningmark
+
+If the **remove samples** option is enabled, samples whose total number of sequences is lower than the specified number will be removed inside the abundance table. 
+
+If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample).
+
+.. class:: h3
+
+Outputs
+
+**Sequence file** (normalised_seed.fasta):
+
+ The normalised sequence file (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
+
+**Abundance file** (normalised_abundance.biom):
+
+ The normalised abundance file. If option **remove samples** has been chosen, then the abundance table will no longer contain information about the removed samples. (format `BIOM &lt;http://biom-format.org/&gt;`_).
+
+**Report file** (report.html):
+
+ Information about discarded data (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
+
+
+.. class:: infomark page-header h2
+
+
+@HELP_CONTACT@
+
+	</help>
+	<expand macro="citations" />
+</tool>