annotate filters.xml @ 0:76c750c5f0d1 draft default tip

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

<?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.
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# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# GNU General Public License for more details.
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# 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_filters" name="FROGS Filters" version="1.3.0">
	<description>Filters OTUs on several criteria.</description>
        <requirements>
                <requirement type="package" version="2.0.1">frogs</requirement>
        </requirements>
        <stdio> 
                <exit_code range="1:" />
                <exit_code range=":-1" />
        </stdio>

	<command>
		filters.py
			--nb-cpus $nb_cpu 
			--input-biom $input_biom  
			--input-fasta $input_fasta
			--output-fasta $output_fasta
			--output-biom $output_biom
			--excluded $output_excluded
			--summary $output_summary
			#if $contaminations_filter.contaminations_filter_isApplied == "yes"
				--contaminant $contaminations_filter.contaminants_db
			#end if	      
			
			#if $abundance_filters.abundance_filters_areApplied == "yes"
				#if $abundance_filters.min_sample_presence
					--min-sample-presence $abundance_filters.min_sample_presence
				#end if
				#if $abundance_filters.min_abundance
					--min-abundance $abundance_filters.min_abundance
				#end if
				#if $abundance_filters.nb_biggest_otu
					--nb-biggest-otu $abundance_filters.nb_biggest_otu
				#end if
			#end if

			#if $RDP_filters.RDP_filters_areApplied == "yes"
				--min-rdp-bootstrap $RDP_filters.rdp_rank:$RDP_filters.rdp_bootstrap
			#end if
		
			#if $blast_filters.blast_filters_areApplied == "yes"
				#if $blast_filters.min_blast_length
					--min-blast-length $blast_filters.min_blast_length
				#end if
				#if $blast_filters.max_blast_evalue
					--max-blast-evalue $blast_filters.max_blast_evalue
				#end if
				#if $blast_filters.min_blast_identity
					--min-blast-identity $blast_filters.min_blast_identity
				#end if
				#if $blast_filters.min_blast_coverage
					--min-blast-coverage $blast_filters.min_blast_coverage
				#end if
			#end if
	</command>
	<inputs>
		<!-- Files -->
		<param format="fasta" name="input_fasta" type="data" label="Sequences file" help="The sequence file to filter (format: fasta)." />
		<param format="biom1" name="input_biom" type="data" label="Abundance file" help="The abundance file to filter (format: BIOM)." />

   		<!-- Parameters -->
		<param name="nb_cpu" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1"></param>
		
		<conditional name="abundance_filters">
			<param name="abundance_filters_areApplied" type="select" label=" *** THE FILTERS ON OTUS IN SAMPLES, OTUS SIZE and SEQUENCE PERCENTAGE" help="If you want to filter OTUs on their abundance and occurrence." >
				<option value="no">No filters</option>
				<option value="yes">Apply filters</option>
			</param>
			<when value="no"></when>
			<when value="yes">
				<param name="min_sample_presence" type="integer" optional="true" label="Minimum number of samples" size="5" help="Fill the field only if you want this treatment. Keep OTU present in at least this number of samples." />
				<param name="min_abundance" type="text" optional="true" label="Minimum proportion/number of sequences to keep OTU" size="5" help="Fill the field only if you want this treatment. Use decimal notation for proportion (example: 0.01 for keep OTU with at least 1% of all sequences) ; Use integer notation for number of sequence (example: 2 for keep OTU with at least 2 sequences, so remove single singleton)." />
				<param name="nb_biggest_otu" type="integer" optional="true" label="N biggest OTU" size="5" help="Fill the fields only if you want this treatment. Keep the N biggest OTU." /> 
			</when>
		</conditional>

		<conditional name="RDP_filters">
			<param name="RDP_filters_areApplied" type="select" label=" *** THE FILTERS ON RDP" help="If you want to filter OTUs on their taxonomic affiliation produced by RDP.">
				<option value="no">No filters</option>
				<option value="yes">Apply filters</option>
			</param>
			<when value="no"></when>
			<when value="yes">
				<param name="rdp_rank" type="select" label="Rank with the bootstrap filter" optional="true">
					<option value="Domain">Domain</option>
					<option value="Phylum">Phylum</option>
					<option value="Class">Class</option>
					<option value="Order">Order</option>
					<option value="Family">Family</option>
					<option value="Genus">Genus</option>
					<option value="Species">Species</option>
   				</param>
				<param name="rdp_bootstrap" type="float" min="0.0" max="1.0" label="Minimum bootstrap % (between 0 and 1)" size="5" optional="true" />
			</when>
		</conditional>

		<conditional name="blast_filters">
			<param name="blast_filters_areApplied" type="select" label=" *** THE FILTERS ON BLAST" help="If you want to filter OTUs on their taxonomic affiliation produced by Blast.">
				<option value="no">No filters</option>
				<option value="yes">Apply filters</option>
			</param>
			<when value="no"></when>
			<when value="yes">
				<param name="max_blast_evalue" type="text" value="" label="Maximum e-value (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" /> 
				<param name="min_blast_identity" type="float" min="0.0" max="1.0" optional="true" label="Minimum identity % (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" />
				<param name="min_blast_coverage" type="float" min="0.0" max="1.0" optional="true" label="Minimum coverage % (between 0 and 1)" size="5" help="Fill the field only if you want this treatment" />
				<param name="min_blast_length" type="integer" optional="true" label="Minimum alignment length" size="5" help="Fill the field only if you want this treatment" />
			</when>
		</conditional>
		
		<conditional name="contaminations_filter">
			<param name="contaminations_filter_isApplied" type="select" label=" *** THE FILTERS ON CONTAMINATIONS" help="If you want to filter OTUs on classical contaminations.">
				<option value="no">No filters</option>
				<option value="yes">Apply filters</option>
			</param>
			<when value="no"></when>
			<when value="yes">
				<param name="contaminants_db" type="select" label="Cotaminant databank" help="The phiX databank (the phiX is a control added in Illumina sequencing technologies).">
		       		<options from_file="phiX_db.loc">
		          		<column name="name" index="0"/>
		          		<column name="value" index="1"/>
		       		</options>
		   		</param>
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="fasta" name="output_fasta" label="${tool.name}: sequences.fasta" from_work_dir="sequences.fasta" />
		<data format="biom1" name="output_biom" label="${tool.name}: abundance.biom" from_work_dir="abundance.biom" />
		<data format="tabular" name="output_excluded" label="${tool.name}: excluded.tsv" from_work_dir="excluded.tsv" />
		<data format="html" name="output_summary" label="${tool.name}: report.html" from_work_dir="report.html" />
	</outputs>
	<tests>
		<test>
	                <param name="input_fasta" value="references/03-chimera.fasta" />
	                <param name="input_biom" value="references/03-chimera.biom" />    
			<conditional name="abundance_filters">
	                        <param name="abundance_filters_areApplied" value="yes" />
				<param name="min_abundance" value="0.00005" />	
				<param name="min_sample_presence" value="3" />
			</conditional>
			<output name="output_fasta" file="references/04-filters.fasta" />
			<output name="output_excluded" file="references/04-filters.excluded" />
	        </test>
	</tests>
	<help>

.. image:: static/images/FROGS_logo.png
   :height: 144
   :width: 110



.. class:: infomark page-header h2

What it does

Filter the OTUs of an abundance table according :

 -The abundance and the occurence of OTUs: presence in samples, OTU size and maximum number of OTUs.

 -The taxonomic affiliation produced by RDP: rank and bootstrap.

 -The taxonomic affiliation produced by Blast: e-value, percentage of identity, percentage of coverage and alignment length.
 
 -Contamination: phiX a control added in Illumina sequencing technologies.



.. 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** (sequences.fasta):

 The sequences after filtering (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).

**Abundance file** (abundance.biom):

 The abundance after filtering (format `BIOM &lt;http://biom-format.org/&gt;`_).

**Excluded file** (excluded.txt):

 The list of the OTUs deleted by filters (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).

**Summary file** (report.html):

 The filters and the number of removed sequences (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).



.. class:: infomark page-header h2

How it works




The OTUs kept are the ones that satisfy into the BIOM input file the thresholds specified by the user.

The BIOM abundance table and the fasta file are written again according to the OTUs kept.

The OTUs discarded are listed in the excluded file.

.. csv-table:: 
   :header: "Steps", "description"
   :widths: 5, 150
   :class: table table-striped

   "1", "Except the filter to select the n most abundant OTUs, all the selected filters are run independently. For each filters an list of the OTUs to remove is generated."
   "2", "All the OTUs tagged to remove by at least one filter are removed."
   "3", "If the filter to select the N most abundant OTUs is filled it is applied."



.. class:: infomark page-header h2

Advices

Please check that the input fasta file and the input BIOM file correspond to the same OTUs.

Examples for the filters on abundance and occurence of the OTUs : 

-To keep the filters that are present in 5 samples, fill the corresponding field with "5".

-To display the 20 biggest OTU, fill the corresponding field with "20".

-To filter on abundance, we advise you to specify 0.005%. It seems to be the optimal threshold (`Bokulich *et al*, 2013 &lt;http://www.nature.com/nmeth/journal/v10/n1/abs/nmeth.2276.html&gt;`_ ).

If you use "FROGS Filters" before "FROGS Affiliation", the filters on RDP and Blast are useless.

----

**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., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf

Depending on the help provided you can cite us in acknowledgements, references or both.
	</help> 
        <citations>
                <citation type="doi">10.1093/bioinformatics/btx791</citation>
                <citation type="doi">10.1128/AEM.01043-13</citation>
                <citation type="doi">10.14806/ej.17.1.200</citation>
                <citation type="doi">10.1093/bioinformatics/btr507</citation>
        </citations>

</tool>