<tool id="rna_star" name="RNA STAR" version="2.4.0d-2">
    <description>Gapped-read mapper for RNA-seq data</description>
    <requirements>
        <requirement type="package" version="2.4.0d">rnastar</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <stdio>
        <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
        <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
        <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
        <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
    </stdio>

    <command><![CDATA[
    ## Create temporary index for custom reference
    #if str($refGenomeSource.genomeSource) == 'history':
        mkdir -p tempstargenomedir &&
        STAR
            --runMode genomeGenerate
            --genomeDir "tempstargenomedir"
            --genomeFastaFiles "$refGenomeSource.ownFile"
            --runThreadN \${GALAXY_SLOTS:-4}
        
        #if str($refGenomeSource.geneModel) != 'None':
            --sjdbOverhang "$refGenomeSource.overhang"
            --sjdbGTFfile "$refGenomeSource.geneModel"
            
            #if str($refGenomeSource.geneModel.ext) == 'gff3':
                --sjdbGTFtagExonParentTranscript Parent
            #end if
        #end if
        ;
    #end if
    
    
    ## Actual alignment
    STAR
    --runThreadN \${GALAXY_SLOTS:-4}
    --genomeLoad NoSharedMemory    
    #if str($refGenomeSource.genomeSource) == 'history':
        --genomeDir "tempstargenomedir"
    #else
        --genomeDir "$refGenomeSource.index.fields.path"
    #end if
    
    --readFilesIn
    #if str($singlePaired.sPaired) == "paired_collection"
        "$singlePaired.input.forward" "$singlePaired.input.reverse"
    #else
        "$singlePaired.input1"
        #if str($singlePaired.sPaired) == "paired"
            "$singlePaired.input2"
        #end if
    #end if

    ## Output parameters
    #if str( $output_params.output_select ) == "yes":
        --outSAMattributes $output_params.outSAMattributes
        --outSAMstrandField $output_params.outSAMstrandField
        --outFilterIntronMotifs $output_params.outFilterIntronMotifs
        #if str( $output_params.output_params2.output_select2 ) == "yes":
            --outSAMunmapped $output_params.output_params2.unmapped_opt
            --outSAMprimaryFlag $output_params.output_params2.primary_opt
            --outSAMmapqUnique "$output_params.output_params2.unique"
            --outFilterType $output_params.output_params2.sjfilter_opt
            --outFilterMultimapScoreRange "$output_params.output_params2.multiScoreRange"
            --outFilterMultimapNmax "$output_params.output_params2.multiNmax"
            --outFilterMismatchNmax "$output_params.output_params2.mismatchNmax"
            --outFilterMismatchNoverLmax "$output_params.output_params2.mismatchNoverLmax"
            --outFilterMismatchNoverReadLmax "$output_params.output_params2.mismatchNoverReadLmax"
            --outFilterScoreMin "$output_params.output_params2.scoreMin"
            --outFilterScoreMinOverLread "$output_params.output_params2.scoreMinOverLread"
            --outFilterMatchNmin "$output_params.output_params2.matchNmin"
            --outFilterMatchNminOverLread "$output_params.output_params2.matchNminOverLread"
        #end if
    #end if

    ## Other parameters
    #if str( $params.settingsType ) == "star_fusion":
        ## Preset parameters for STAR-Fusion
##        --twopass1readsN 100000000
##        --sjdbOverhang 100
        --outReadsUnmapped None
        --chimSegmentMin 12
        --chimJunctionOverhangMin 12
        --alignSJDBoverhangMin 10
        --alignMatesGapMax 200000
        --alignIntronMax 200000
        ## --chimSegmentReadGapMax 3              ## not an option in STAR 2.4.0
        ## --alignSJstitchMismatchNmax 5 -1 5 5   ## not an option in STAR 2.4.0

    #elif str( $params.settingsType ) == "full":
        ## Extended parameter options

        ## Seed parameter options
        #if str( $params.seed.seed_select ) == "yes":
            --seedSearchStartLmax "$params.seed.searchStart"
            --seedSearchStartLmaxOverLread "$params.seed.searchStartNorm"
            --seedSearchLmax "$params.seed.searchLmax"
            --seedMultimapNmax "$params.seed.multimap"
            --seedPerReadNmax "$params.seed.readMax"
            --seedPerWindowNmax "$params.seed.windowMax"
            --seedNoneLociPerWindow "$params.seed.oneSeed"
        #end if

        ## Alignment parameter options
        #if str( $params.align.align_select ) == "yes":
            --alignIntronMin "$params.align.intronMin"
            --alignIntronMax "$params.align.intronMax"
            --alignMatesGapMax "$params.align.gapMax"
            --alignSJoverhangMin "$params.align.sjOverhang"
            --alignSJDBoverhangMin "$params.align.sjdbOverhang"
            --alignSplicedMateMapLmin "$params.align.splicedMate"
            --alignSplicedMateMapLminOverLmate "$params.align.splicedMateNorm"
            --alignWindowsPerReadNmax "$params.align.windows"
            --alignTranscriptsPerWindowNmax "$params.align.transWindow"
            --alignTranscriptsPerReadNmax "$params.align.transRead"
            --alignEndsType $params.align.endsType_opt
        #end if

        ## Chimeric alignment parameter options
        #if str( $params.chim.chim_select ) == "yes":
            --chimSegmentMin "$params.chim.segmentMin"
            --chimScoreMin "$params.chim.scoreMin"
            --chimScoreDropMax "$params.chim.scoreDrop"
            --chimScoreSeparation "$params.chim.scoreSep"
            --chimScoreJunctionNonGTAG "$params.chim.scoreJunction"
            --chimJunctionOverhangMin "$params.chim.junctionOverhang"
        #end if

    #end if

    ## BAM conversion.
    
    ## Convert aligned reads.
    && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Aligned.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - AlignedSorted 2>/dev/null
    
    ## Convert chimeric reads.
    #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.segmentMin) > 0 ):
        && samtools view -@ \${GALAXY_SLOTS:-4} -Shb Chimeric.out.sam | samtools sort -@ \${GALAXY_SLOTS:-4} - ChimericSorted 2>/dev/null
    #end if
    ]]></command>

    <inputs>
        <!-- FASTQ input(s) and options specifically for paired-end data. -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Single-end or paired-end reads">
              <option value="single" selected="true">Single-end</option>
              <option value="paired">Paired-end (as individual datasets)</option>
              <option value="paired_collection">Paired-end (as collection)</option>
            </param>
            <when value="single">
                <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
            </when>
            <when value="paired">
                <param format="fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
                <param format="fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
            </when>
            <when value="paired_collection">
                <param format="fastq,fasta" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
            </when>
        </conditional>

        <!-- Genome source. -->
        <conditional name="refGenomeSource">
            <param name="genomeSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
                <option value="indexed" selected="True">Use a built-in index</option>
                <option value="history">Index and use a genome fasta and GTF file from history</option>
            </param>
            <when value="indexed">
            <param name="index" type="select" label="Select a reference genome">
                <options from_data_table="rnastar_index">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                </options>
            </param>
            </when>
            <when value="history">
                <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
                <param name="geneModel" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions. Leave blank for none"
                    optional="true" help="Optional. If supplied, the index file will retain exon junction information for mapping splices (--sjdbGTFfile)"/>
                <param name="overhang" type="integer" min="0" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1 (--sjdbOverhang)"/>
            </when>
        </conditional>
        
        <!-- Output parameter settings. -->
        <conditional name="output_params">
          <param name="output_select" type="select" label="Would you like to set output parameters (formatting and filtering)?">
            <option value="no" selected="true">No</option>
            <option value="yes">Yes</option>
          </param>
          <when value="yes">
            <param name="outSAMattributes" type="select" label="Extra SAM attributes to include" help="See &quot;Extra SAM attributes&quot; below (--outSAMattributes)">
              <option value="Standard" selected="true">Standard</option>
              <option value="All">All</option>
              <option value="None">None</option>
            </param>
            <param name="outSAMstrandField" type="select" label="Include strand field flag XS" help="For Cufflinks compatibility with unstranded RNA-seq data, this option is required (--outSAMstrandField)">
              <option value="None" selected="true">No</option>
              <option value="intronMotif">Yes -- and reads with inconsistent and/or non-canonical introns are filtered out</option>
            </param>
            <param name="outFilterIntronMotifs" type="select" label="Filter alignments containing non-canonical junctions" help="For Cufflinks compatibility, removing alignments with non-canonical junctions is recommended (--outFilterIntronMotifs)">
              <option value="None" selected="true">No</option>
              <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>
              <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option>
            </param>

            <!-- Additional output parameter settings. -->
            <conditional name="output_params2">
              <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
              </param>
              <when value="yes">
                <param name="unmapped_opt" type="boolean" truevalue="Within" falsevalue="None" checked="false" label="Would you like unmapped reads included in the SAM?" help="(--outSAMunmapped)"/>
                <param name="primary_opt" type="boolean" truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" label="Would you like all alignments with the best score labeled primary?" help="(--outSAMprimaryFlag)"/>
                <param name="unique" type="integer" value="255" min="0" max="255" label="MAPQ value for unique mappers" help="(--outSAMmapqUnique)"/>
                <param name="sjfilter_opt" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?" help="(--outFilterType)"/>
                <param name="multiScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments" help="(--outFilterMultimapScoreRange)"/>
                <param name="multiNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output (--outFilterMultimapNmax)"/>
                <param name="mismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output (--outFilterMismatchNmax)"/>
                <param name="mismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output (--outFilterMismatchNoverLmax)"/>
                <param name="mismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output (--outFilterMismatchNoverReadLmax)"/>
                <param name="scoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output (--outFilterScoreMin)"/>
                <param name="scoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output (--outFilterScoreMinOverLread)"/>
                <param name="matchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output (--outFilterMatchNmin)"/>
                <param name="matchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output (--outFilterMatchNminOverLread)"/>
              </when>
              <when value="no"/>
            </conditional>

          </when>
          <when value="no"/>
        </conditional>

        <!-- Other parameter settings. -->
        <conditional name="params">
          <param name="settingsType" type="select" label="Other parameters (seed, alignment, and chimeric alignment)">
            <option value="default" selected="true">Use Defaults</option>
            <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
            <option value="full">Extended parameter list</option>
          </param>
          <when value="default"/>
          <when value="star_fusion"/> <!-- Set STAR-fusion parameters automatically -->

          <when value="full">

            <!-- Seed parameters -->
            <conditional name="seed">
              <param name="seed_select" type="select" label="Would you like to set seed parameters?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
              </param>
              <when value="yes">
                <param name="searchStart" type="integer" min="1" value="50" label="Search start point through the read" help="(--seedSearchStartLmax)"/>
                <param name="searchStartNorm" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length" help="(--seedSearchStartLmaxOverLread)"/>
                <param name="searchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length (--seedSearchLmax)"/>
                <param name="multimap" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching" help="(--seedMultimapNmax)"/>
                <param name="readMax" type="integer" min="1" value="1000" label="Maximum number of seeds per read" help="(--seedPerReadNmax)"/>
                <param name="windowMax" type="integer" min="1" value="50" label="Maximum number of seeds per window" help="(--seedPerWindowNmax)"/>
                <param name="oneSeed" type="integer" min="1" value="10" label="Maximum number of one seed loci per window" help="(--seedNoneLociPerWindow)"/>
              </when>
              <when value="no"/>
            </conditional>

            <!-- Alignment parameters -->
            <conditional name="align">
              <param name="align_select" type="select" label="Would you like to set alignment parameters?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
              </param>
              <when value="yes">
                <param name="intronMin" type="integer" min="0" value="21" label="Minimum intron size" help="(--alignIntronMin)"/>
                <param name="intronMax" type="integer" min="0" value="0" label="Maximum intron size" help="(--alignIntronMax)"/>
                <param name="gapMax" type="integer" min="0" value="0" label="Maximum gap between two mates" help="(--alignMatesGapMax)"/>
                <param name="sjOverhang" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments" help="(--alignSJoverhangMin)"/>
                <param name="sjdbOverhang" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments" help="(--alignSJDBoverhangMin)"/>
                <param name="splicedMate" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced" help="(--alignSplicedMateMapLmin)"/>
                <param name="splicedMateNorm" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length" help="(--alignSplicedMateMapLminOverLmate)"/>
                <param name="windows" type="integer" min="1" value="10000" label="Maximum number of windows per read" help="(--alignWindowsPerReadNmax)"/>
                <param name="transWindow" type="integer" min="1" value="100" label="Maximum number of transcripts per window" help="(--alignTranscriptsPerWindowNmax)"/>
                <param name="transRead" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider" help="(--alignTranscriptsPerReadNmax)"/>
                <param name="endsType_opt" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?" help="(--alignEndsType)"/>
              </when>
              <when value="no"/>
            </conditional>

            <!-- Chimeric alignment parameters -->
            <conditional name="chim">
              <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
              </param>
              <when value="yes">
                <param name="segmentMin" type="integer" min="0" value="0" label="Minimum length of chimeric segment" help="Default of 0 means no chimeric output (--chimSegmentMin)"/>
                <param name="scoreMin" type="integer" min="0" value="0" label="Minimum total (summed) score of chimeric segments" help="(--chimScoreMin)"/>
                <param name="scoreDrop" type="integer" min="0" value="20" label="Maximum difference of chimeric score from read length" help="(--chimScoreDropMax)"/>
                <param name="scoreSep" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one" help="(--chimScoreSeparation)"/>
                <param name="scoreJunction" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction" help="(--chimScoreJunctionNonGTAG)"/>
                <param name="junctionOverhang" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction" help="(--chimJunctionOverhangMin)"/>
              </when>
              <when value="no"/>
            </conditional>

          </when>
        </conditional>
        
    </inputs>

    <outputs>
        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
        <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: starchimjunc" from_work_dir="Chimeric.out.junction">
            <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter>
            <actions>
                <conditional name="refGenomeSource.genomeSource">
                    <when value="indexed">
                        <action type="metadata" name="dbkey">
                            <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                            </option>
                        </action>
                    </when>
                    <when value="history">
                        <action type="metadata" name="dbkey">
                            <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>

        <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: starmappedchim.bam" from_work_dir="ChimericSorted.bam">
            <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['segmentMin'] > 0 )</filter>
            <actions>
                <conditional name="refGenomeSource.genomeSource">
                    <when value="indexed">
                        <action type="metadata" name="dbkey">
                            <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                            </option>
                        </action>
                    </when>
                    <when value="history">
                        <action type="metadata" name="dbkey">
                            <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        
        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: starsplicejunct.bed" from_work_dir="SJ.out.tab">
            <actions>
                <conditional name="refGenomeSource.genomeSource">
                    <when value="indexed">
                        <action type="metadata" name="dbkey">
                            <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                            </option>
                        </action>
                    </when>
                    <when value="history">
                        <action type="metadata" name="dbkey">
                            <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
        
        <data format="bam" name="mapped_reads" label="${tool.name} on ${on_string}: starmapped.bam" from_work_dir="AlignedSorted.bam">
            <actions>
                <conditional name="refGenomeSource.genomeSource">
                    <when value="indexed">
                        <action type="metadata" name="dbkey">
                            <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                            </option>
                        </action>
                    </when>
                    <when value="history">
                        <action type="metadata" name="dbkey">
                            <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                        </action>
                    </when>
                </conditional>
            </actions>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value="tophat_test.fa" />
            <param name="sPaired" value="single" />

            <param name="output_select" value="yes" />
            <param name="outSAMattributes" value="All" />
            <param name="outSAMstrandField" value="intronMotif" />
            <param name="settingsType" value="default" />
            
            <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff = "10"/>
            <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
            <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />
        </test>
        <test>
            <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value="tophat_test.fa" />
            <param name="sPaired" value="single" />
            
            <param name="output_select" value="yes" />
            <param name="outSAMattributes" value="All" />
            <param name="outSAMstrandField" value="intronMotif" />
            <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
            
            <param name="output_select2" value="yes" />
            <param name="scoreMinOverLread" value="0.9" />
            <param name="settingsType" value="full" />
            <param name="seed_select" value="yes" />
            <param name="searchStart" value="25" />

            <output name="output_log" file="rnastar_test2.log" compare="diff" lines_diff="10"/>
            <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/>
            <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
        </test>

        <test>
            <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value="test3.ref.fa" />
            <param name="sPaired" value="single" />

            <param name="output_select" value="yes" />
            <param name="outSAMattributes" value="All" />
            <param name="outSAMstrandField" value="intronMotif" />
            <param name="settingsType" value="star_fusion" />
            
            <output name="chimeric_junctions" file="test3.chimjunc.tabular"/>
        </test>
        
        <test>
            <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
            <param name="genomeSource" value="history" />
            <param name="ownFile" value="tophat_test.fa" />
            <param name="sPaired" value="single" />
            
            <param name="output_select" value="yes" />
            <param name="outSAMattributes" value="All" />
            <param name="outSAMstrandField" value="intronMotif" />
            <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
            
            <param name="output_select2" value="yes" />
            <param name="settingsType" value="full" />
            <param name="seed_select" value="yes" />
            <param name="align_select" value="yes" />
            <param name="chim_select" value="yes" />
            
            <!-- Uses default settings, should be similar to test1, but tests the parameters -->
            <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="10"/>
            <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
            <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /><!-- header is 434 bytes larger  -->
        </test>

    </tests>
    <help>
**What it does**

This tool runs STAR, an ultrafast universal RNA-seq aligner.

**Extra SAM attributes**

The Standard option includes the following four attributes::

  NH: Number of reported alignments that contain the query in the current record.
  HI: Query hit index, indicating the alignment record is the i-th one stored in SAM
  AS: Local alignment score (paired for paired-end reads)
  nM: Number of mismatches per (paired) alignment

The All option includes the Standard attributes, plus the following four::

  NM: Edit distance to the reference, including ambiguous bases but excluding clipping
  MD: String for mismatching positions
  jM: Intron motifs for all junctions
  jI: Start and end of introns for all junctions

**STAR-Fusion**

STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running
STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::

  --twopassMode Basic                   # not an option in STAR 2.4.0
  --chimSegmentReadGapMax 3             # not an option in STAR 2.4.0
  --alignSJstitchMismatchNmax 5 -1 5 5  # not an option in STAR 2.4.0

**Attributions**

Note that each component has its own license:
 - RNA STAR: GPLv3
 - samtools: MIT/Expat License

rna_star - see the web site at rna_star_

For details, please see the rna_starMS_
"STAR: ultrafast universal RNA-seq aligner"
A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635

Galaxy_ (that's what you are using right now!) for gluing everything together

Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper

Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
and odds and ends of other code and documentation comprising this tool was
written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts

.. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
.. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
.. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
.. _rna_star: https://github.com/alexdobin/STAR
.. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full
.. _Galaxy: http://getgalaxy.org
</help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/bts635</citation>
    </citations>
</tool>