view normalisation.xml @ 7:76dcbe930b1d draft

"planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 0a8dfe386b79711c479cf8a2bc8e9677e521b9e5-dirty"

<?xml version="1.0"?>
<!--
# Copyright (C) 2015 INRA
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# 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
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-->
<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy2">
        <description>Normalise OTUs abundance.</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="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 normalise (format: fasta)." />
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="Abundance file to normalise (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="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" />
		<data format="biom1" name="output_biom" label="${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"/>
        	<param name="num_reads" value="100"/>
            <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 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.


@HELP_CONTACT@

	</help>

	<citations>
		<expand macro="citations" />
	</citations>
	
</tool>