<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="3.0.0-0">
    <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
    <requirements>
        <requirement type="package" version="3.0.0">flaimapper</requirement>
    </requirements>

    <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>

    <command detect_errors="exit_code"><![CDATA[
        flaimapper
            -v
            -f '${output_select.output_format}'
            -o '${output}'

            #if $output_select.output_format == '1':
                #if $output_select.fasta:
                    -r '${output_select.fasta}'
                #end if
            #else
                --offset5p ${output_select.offset5p}
                --offset3p ${output_select.offset3p}
            #end if

            #if $parameters:
                -p '${parameters}'
            #end if

            '${alignment}'
    ]]></command>

    <inputs>
        <param name="alignment" type="data" format="bam" multiple="false"
               label="Alignment file"
               help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />

        <conditional name="output_select">
            <param name="output_format" type="select" label="Output format" argument="-f">
                <option value="1">Tabular</option>
                <option value="2">GTF</option>
            </param>

            <when value="1">
                <param name="fasta" type="data" format="fasta" optional="true"
                       label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
                       help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
            </when>

            <when value="2">
                <param name="offset5p" type="integer" value="4"
                       label="Add 5'-offset to exon-type entry in GTF output file"
                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset5p" />
                <param name="offset3p" type="integer" value="4"
                       label="Add 3'-offset to exon-type entry in GTF output file"
                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
            </when>
        </conditional>

        <param name="parameters" type="data" format="txt,tabular" optional="true"
               label="(Optional) Custom parameters file" help="" argument="-p" />

    </inputs>

    <outputs>
        <data format="tabular" name="output"
              label="${tool.name} on $on_string">
            <change_format>
                <when input="output_select.output_format" value="1" format="tabular" />
                <when input="output_select.output_format" value="2" format="gtf" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <!-- tabular -->
        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
        <test>
            <param name="alignment" value="snord81.bam" ftype="bam" />
            <param name="fasta" value="snord81.fa" ftype="fasta" />
            <param name="output_format" value="1" />

            <output name="output" file="snord81.flaimapper.txt" />
        </test>
        <test>
            <param name="alignment" value="snord81.bam" ftype="bam" />
            <param name="output_format" value="1" />

            <output name="output" file="snord81.flaimapper.no-seq.txt" />
        </test>
        <!-- Testing "Full genome alignment"-type analysis -->
        <test>
            <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
            <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
            <param name="output_format" value="1" />

            <output name="output" file="test_genomic_flaimapper_output.txt" />
        </test>
        <test>
            <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
            <param name="output_format" value="1" />

            <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
        </test>

        <!-- GTF -->
        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
        <test>
            <param name="alignment" value="snord81.bam" ftype="bam" />
            <param name="output_format" value="2" />

            <output name="output" file="snord81.flaimapper.gtf" />
        </test>
        <!-- Testing "Full genome alignment"-type analysis -->
        <test>
            <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
            <param name="output_format" value="2" />

            <output name="output" file="test_genomic_flaimapper_output.gtf" />
        </test>

        <!-- test custom parameters -->
        <test>
            <param name="alignment" value="snord81.bam" ftype="bam" />
            <param name="output_format" value="2" />
            <param name="offset5p" value="5" />
            <param name="offset3p" value="5" />

            <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
        </test>
        <test>
            <param name="alignment" value="snord81.bam" ftype="bam" />
            <param name="output_format" value="2" />
            <param name="parameters" value="filter-parameters.duck.15.txt"/>

            <output name="output" file="snord81.flaimapper.duck-15.gtf" />
        </test>
        
        <!-- Tests a new feature that allows multiple fragments of different size, starting at one identical positions -->
        <test>
            <param name="alignment" value="multilength_fragments_per_position_001.bam" ftype="bam" />
            <param name="output_format" value="1" />

            <output name="output" file="multilength_fragments_per_position_001.txt" />
        </test>
    </tests>

    <help><![CDATA[
FlaiMapper wrapper for Galaxy
=============================

Fragment Location Annotation Identification Mapper

FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.


Input
-----

Alignment
*********

This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.

Prior to running FlaiMapper, it is common to align sequencing reads to either:

- mature ncRNA sequences
- all chromosomes

Example- and reference data
***************************

The reference sequence should be provided in FASTA format.

You can access **ncRNAdb09** FASTA file at the following URL:
https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*

If you want to test FlaiMapper with example data you can obtain several
alignment files from the following directory tree:

https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments

More details are given in the manual at the following website:

https://github.com/yhoogstrate/flaimapper
    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btu696</citation>
    </citations>
</tool>