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<tool id="paqmir_postprocess_quantifier" name="PAQmiR Postprocess Quantifier" version="1.0.0">
	<description>filters results to quantify, annotate, and eliminate redundancy in miRNAs</description>
	<stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <!-- In case the return code has not been set propery check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
	<command interpreter="bash">
	<![CDATA[
		postprocess_quantifier.sh $res_quantifier $miRBase $mature_and_new_mapped $option.filtre $nbCondition 
                #if $option.filtre=="yes"
			$option.valeur_filtre
                #else 
			1
		#end if
	]]>
	</command>
       	<inputs>
		<param name="res_quantifier" format="tabular" type="data" label="Quantification file" help="Tabular quantification file from Quantifier"/>
		<param name="miRBase" format="tabular" type="data" label="MiRBase.mrd file" help="MiRBase.mrd file from Quantifier"/>
		<param name="mature_and_new_mapped" format="tabular" type="data" label="MiRNA mapping" help="Reference matures against precursors. Mapping file from quantifier in ARF format"/>
		<param name="nbCondition" format="txt" size="30" value="1" type="integer" min="1" max="99" label="Total number of sample processed" help="Number of read sets used in the initial mapping step (Mapper)"/>
		<conditional name="option">
                        <param name="filtre" type="boolean" truevalue="yes" falsevalue="no" label="Apply read count filter?"/>
			<when value="no">
			</when>
			<when value="yes">
				<param name="valeur_filtre" format="txt" size="30" value="1" type="integer" label="Minimal read count" help="Minimal read count per sample"/>
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data name="miRNAs_expressed_all_samples.pre_uniq" format="tabular" from_work_dir="miRNAs_expressed_all_samples.pre_uniq.csv" label="miRNAs_expressed_all_samples.pre_uniq.csv"/>
		<data name="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq" format="tabular" from_work_dir="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv" label="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv"/>
		<data name="annotation_statistics" format="txt" from_work_dir="annotation_statistics.txt" label="annotation_statistics.txt"/>
	</outputs>
        <!--tests> Don't work with "from_work_dir"
            <test>
                 <param name="res_quantifier" value="quantifier_output.tsv"/>
                 <param name="miRBase" value="miRBase.mrd"/>
                 <param name="mature_and_new_mapped" value="matures_and_new_predicted_matures.fa_mapped.arf"/>
                 <param name="nbCondition" value="3"/>
                 <param name="valeur_filtre" value="1"/>

                 <output name="miRNAs_expressed_all_samples.pre_uniq" file="miRNAs_expressed_all_samples.pre_uniq.csv"/>
                 <output name="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq" file="miRNAs_expressed_all_samples.pre_uniq.matureSEQ_uniq.csv"/>
                 <output name="annotation_statistics" file="annotation_statistics.txt"/>
            </test>
        </tests-->
	<help>
<![CDATA[

        | This tool is part of the workflow **PAQmiR** for the *Prediction Annotation and Quantification of miRNA with miRDeep2*
	|
	| Wrappers are the product of Valentin Marcon, Kevin Normand & Sylvain Marthey (Thanks to INRA Migale, IFB ressources & INRA GABI)


**What it does**
This module assigns mature miRNAs to a set of precursors, and report the quantification of the best two mature (3p & 5p predicted from their position on the precursor) observed for each precursor.
The module uses output files provided by the quantifier.pl module from miRdeep2 and assigns the matures to the precursors by using the following order of priority:

	| - Mature known in the species studied (generaly all matures from miRBase known for the species are used)
        | - Mature known in another species (all mature from miRBase, or only those corresponding to a subset of closely related species are used). In case where several mature are detected, mature with the highest count is chosen.
        | - Mature unknown (generaly matures predicted by miRDeep2.pl module are used)

**Input**

	| - Standard results file of Quantifier
        | - MiRBase.mrd file produced by Quantifier
	| - Mapping of miRNAs file

**Output**

	| - Quantification pre_uniq file :  tabular file containing the quantification of the two tbest matures (3p & 5p) observed for each precursor.
	| - Quantification matureSeq_uniq file : tabular subpart of file pre_uniq containing only one quantification per mature sequence.
	| - Annotation statistics : Txt file containing statistics about annotation process
]]>
	</help>
	<citations>
                <citation type="doi">10.1371/journal.pone.0091938</citation>
                <citation type="doi">10.1186/s12864-015-1471-y</citation>
	        <citation type="doi">10.1093/nar/gkr688</citation>
        	<citation type="doi">10.1002/0471250953.bi1210s36</citation>
        </citations>
</tool>