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<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="1.1.0">
	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
	<requirements>
		<requirement type="package" version="1.1.0">flaimapper</requirement>
		<requirement type="package" version="0.7.7">pysam</requirement>
	</requirements>
	<command>
		##rm $mask".tbi"
		##rm $fasta".fai"
		
		flaimapper
			 -v
			 -f $output_format
			 -o $output
			 -m $mask
			 -r $fasta
			#for $alignment in $alignments
				$alignment
			#end for
	</command>
	
	<version_command>flaimapper --version</version_command>
	
	<inputs>
		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
		
		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
		
		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
		
		<param name="output_format" type="select" label="Output format">
			<option value="1">Tabular (1 fragment per column)</option>
			<option value="2">Tabular  (1 precursor per column)</option>
			<option value="3">GenBank</option>
			<!-- option value="gtf">GTF/GFF</option -->
		</param>
	</inputs>
	
	<outputs>
		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
	</outputs>
	
	<help>
		FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
		
		doi:10.1093/bioinformatics/btu696
	</help>
</tool>