<tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0">
    <description>
<![CDATA[
identification of novel and known miRNAs
]]>
    </description>
    <requirements>
        <requirement type="package" version="2.0">mirdeep2</requirement>
        <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="5.18.1">perl</requirement>
        <requirement type="package" version="1.8.5">vienna_rna</requirement>
        <requirement type="package" version="2.023">pdf_api2</requirement>
        <requirement type="package" version="2.0">randfold</requirement>
    </requirements>

    <command>
<![CDATA[
    miRDeep2.pl
    
    $reads
    $genome
    $mappings
    
    #if $mature_this
        $mature_this
    #else
        none
    #end if
    
    #if $mature_other
        $mature_other
    #else
        none
    #end if
    
    #if $precursors
        $precursors
    #else
        none
    #end if
    
    #if $species.value != 'all'
        -t $species
    #end if
    
    #if $star_sequences
        -s $star_sequences
    #end if
    
    #if $min_read_stack
        -a $min_read_stack
    #end if
    
    #if $min_read_stack
        -a $min_read_stack
    #end if
    
    -g $max_precursors_analyze
    -b $min_score_cutoff
    $disable_randfold
    
    ; mv result*.bed result.bed 2> /dev/null
    ; mv result*.csv result.csv 2> /dev/null
    ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
    ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
    
    ## html output
    ;
    mv result*.html $html 2> /dev/null
    
    ## move pdf directory to be accessible from the new index.html
    ;
    mkdir -p $html.files_path 2> /dev/null
    ;
    mv pdfs* $html.files_path 2> /dev/null
    
]]>
    </command>
    <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>
    <inputs> 
        <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads">
            <help>
<![CDATA[
Reads in fasta format. The identifier should contain a prefix, a running
number and a '_x' to indicate the number of reads that have this sequence.
There should be no redundancy in the sequences.
]]>
            </help>
        </param>
        <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/>
        <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/>
        <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species" 
            help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/>
        <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species">
            <help>
<![CDATA[
miRBase miRNA sequences in fasta format. These should be the pooled known
mature sequences for 1-5 species closely related to the species being analyzed.
]]>
            </help>
        </param>
        <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences" 
            help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/>
            
        <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)">
            <option value="all">All species</option>
            <option value="tni">tetraodon</option>
            <option value="dps">d.pseudoobscura</option>
            <option value="dya">d.yakuba</option>
            <option value="ame">a.mellifera</option>
            <option value="dmo">d.mojavensis</option>
            <option value="cel">worm</option>
            <option value="aga">a.gambiae</option>
            <option value="cbr">c.briggsae</option>
            <option value="cin">c.intestinalis</option>
            <option value="mmu">mouse</option>
            <option value="xtr">x.tropicalis</option>
            <option value="eca">horse</option>
            <option value="cfa">dog</option>
            <option value="fru">fugu</option>
            <option value="bta">cow</option>
            <option value="der">d.erecta</option>
            <option value="dgr">d.grimshawi</option>
            <option value="gga">chicken</option>
            <option value="spu">s.purpuratus</option>
            <option value="bfl">lancelet</option>
            <option value="ptr">chimp</option>
            <option value="dse">d.sechellia</option>
            <option value="dpe">d.persimilis</option>
            <option value="dvi">d.virilis</option>
            <option value="rno">rat</option>
            <option value="dme">d.melanogaster</option>
            <option value="lca">cat</option>
            <option value="sja">c.japonica</option>
            <option value="dan">d.ananassae</option>
            <option value="hsa">human</option>
            <option value="dsi">d.simulans</option>
        </param>
        <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
        
        <param name="min_read_stack" optional="true" type="integer" minvalue="0" label="Minimum read stack height">
            <help>
<![CDATA[
minimum read stack height that triggers analysis. Using this option disables
automatic estimation of the optimal value and all detected precursors are analyzed. (-a)
]]>
            </help>
        </param>
        <param name="max_precursors_analyze" type="integer" value="50000" label="Maximum precursors" 
            help="Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g)."/>
        <param name="min_score_cutoff" type="integer" value="0" label="Minimum miRNA score" 
            help="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)"/>
        <param name="disable_randfold" type="boolean" truevalue="-c" falsevalue="" label="Disable randfold analysis" help="(-c)"/>
    </inputs>
    <outputs>
        <data name="tab_results" format="tabular" from_work_dir="result.csv" label="Tabular output of ${tool.name} on ${on_string}"/>
        <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
        <data name="pred_acc" format="tabular" from_work_dir="survey.csv" label="Prediction accuracy output of ${tool.name} on ${on_string}"/>
        <data name="bed_out" format="bed" from_work_dir="result.bed" label="Bed output of ${tool.name} on ${on_string}"/>
        <data name="mrd_out" format="txt" from_work_dir="output.mrd" label="Text output of ${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="reads" value="reads_collapsed.fa"/>
            <param name="genome" value="cel_cluster.fa"/>
            <param name="mappings" value="reads_collapsed_vs_genome.arf"/>
            <param name="mature_this" value="mature_ref_this_species.fa"/>
            <param name="mature_other" value="mature_ref_other_species.fa"/>
            <param name="precursors" value="precursors_ref_this_species.fa"/>
            
            <output name="tab_results" file="result.csv" compare="sim_size"/>
            <output name="prec_acc" file="survey.csv" compare="sim_size"/>
            <output name="bed_out" file="result.bed" compare="sim_size"/>
            <output name="mrd_out" file="output.mrd" compare="sim_size"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What MiRDeep2 does**

MiRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples.
]]>
    </help>
    <citations>
        <citation type="doi">10.1093/nar/gkr688</citation>
        <citation type="doi">10.1002/0471250953.bi1210s36</citation>
    </citations>
</tool>