<tool id="trinity" name="Trinity" version="2.0.6">
    <description>de novo assembly of RNA-Seq data</description>
    <requirements>
        <requirement type="package" version="2.0.6">trinity</requirement>
        <requirement type="package" version="1.1.2">bowtie</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
        <requirement type="set_environment">TRINITY_MAX_MEMORY</requirement>
    </requirements>
    <command><![CDATA[
       Trinity

        ## Inputs.
        #if $inputs.paired_or_single == "paired":
            --left $inputs.left_input --right $inputs.right_input
            
            #if $inputs.left_input.is_of_type('fasta'):
                --seqType fa
            #else:
                --seqType fq
            #end if
            
            #if $inputs.strand.is_strand_specific:
                --SS_lib_type $inputs.strand.library_type
            #end if
            
            $inputs.jaccard_clip

        #else:
            --single $inputs.input
            
            #if $inputs.input.is_of_type('fasta'):
                --seqType fa
            #else:
                --seqType fq
            #end if
            
            #if $inputs.strand.is_strand_specific:
                --SS_lib_type $inputs.strand.library_type
            #end if
        #end if
            
        $norm

        ## Additional parameters.
        #if $additional_params.min_contig_length:
            --min_contig_length $additional_params.min_contig_length
        #end if
        #if $additional_params.long_reads:
            --long_reads $additional_params.long_reads
        #end if
        #if $additional_params.guided.is_guided == "yes" and $additional_params.guided.genome_guided_bam:
            --genome_guided_bam $additional_params.guided.genome_guided_bam

            #if $additional_params.guided.genome_guided_min_coverage:
                --genome_guided_min_coverage $additional_params.guided.genome_guided_min_coverage
            #end if

            #if $additional_params.guided.genome_guided_min_reads_per_partition:
                --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition
            #end if
            
        #end if

        ## CPU and butterfly options.
        --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS} --bfly_opts "-V 10 --stderr"
        
         > $trinity_log 2>&1

    ]]></command>
    <inputs>
        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
            </param>
            <when value="paired">
                <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
                <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
                <conditional name="strand">
                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                    <when value="false">
                    </when>
                    <when value="true">
                        <param name="library_type" type="select" label="Strand-specific Library Type">
                            <option value="FR">Forward-Reverse</option>
                            <option value="RF">Reverse-Forward</option>
                        </param>
                    </when>
                </conditional>
                <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
                <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/>
            </when>
            <when value="single">
                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
                <conditional name="strand">
                    <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/>
                    <when value="false">
                    </when>
                    <when value="true">
                        <param name="library_type" type="select" label="Strand-specific Library Type">
                            <option value="F">F</option>
                            <option value="R">R</option>
                        </param>
                    </when>
                </conditional>
            </when>
        </conditional>
        
        <param name="norm" type="boolean" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/>

        <section name="additional_params" title="Additional Options" expanded="False">
            <param name="min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/>
            
            <conditional name="guided">
                <param name="is_guided" type="select" label="Use the genome guided mode?" help="">
                    <option value="no">No</option>
                    <option value="yes">Yes</option>
                 </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param format="bam" name="genome_guided_bam" type="data" optional="true" label="Genome guided BAM file" help="If you already mapped the reads to the genome, trinity can use this information"/>
                    <param name="genome_guided_min_coverage" type="integer" optional="true" value="1" min="1" label="Minimum read coverage for identifying an expressed region of the genome"/>
                    <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/>
                </when>
            </conditional>
            
            
            <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/>
        </section>
    </inputs>
    <outputs>
        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </outputs>
    <tests>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>
            <param name="right_input" value="reads.right.fq"/>
            <param name="is_strand_specific" value="true"/>
            <param name="norm" value="false"/>
            <param name="library_type" value="RF"/>
            <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" />
        </test>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>
            <param name="right_input" value="reads.right.fq"/>
            <param name="is_strand_specific" value="true"/>
            <param name="norm" value="true"/>
            <param name="library_type" value="RF"/>
            <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" />
        </test>
    </tests>
    <help>
        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.

        .. _Trinity: http://trinityrnaseq.github.io
    </help>
    
     <citations>
        <citation type="doi">doi:10.1038/nbt.1883</citation>
    </citations>
</tool>