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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit 38b164ccb9b3cdfb58d83cdc1f05063a40123bab-dirty

<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
    <description>detect fusion genes in RNA-Seq data</description>
    <requirements>
        <!-- Bio-conda -->
        <requirement type="package" version="0.5.4">star-fusion</requirement>
    </requirements>

    <stdio>
        <regex match="command not found" source="stderr" level="fatal"/>
        <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
        <regex match="FATAL ERROR" source="stderr" level="fatal"/>
        
        <regex match="Warning:" source="stderr" level="warning"/>
        <regex match="CMD:" source="stderr" level="warning"/>
        
        <regex match="-done creating index file:" source="stderr" level="warning"/>
        <regex match="-parsing GTF file:" source="stderr" level="warning"/>
        <regex match="-building interval tree" source="stderr" level="warning"/>
        <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>
        <regex match="-mapping reads to genes" source="stderr" level="warning"/>
        <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>
        
        <regex match="Process complete" source="stderr" level="warning"/>
    </stdio>

    <version_command>STAR-Fusion --version  2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>

    <command><![CDATA[
        ## 1. do blastn on the genome reference
        if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then
            gzip_suffix='' ;
        else
            ## Older versions of gzip do not support the -k option to keep
            ## the original file - this should be an universion solution
            
            gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' &&
            gzip_suffix='.gz' ;
        fi &&
        
        ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
        prep_genome_lib.pl
            --genome_fa '${fasta_type.ownFile}'
            --gtf '${geneModel}'
            --blast_pairs "${blast_pairs}\$gzip_suffix"
            --CPU \${GALAXY_SLOTS:-1}
            --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
        &&
        
        ## 3. Run STAR-Fusion
        STAR-Fusion

            #if str($input_params.input_source) == "use_chimeric":
                --chimeric_junction '${input_params.chimeric_junction}'
            #else:
                --left_fq '${input_params.left_fq}'
                #if $input_params.right_fq:
                    --right_fq '${input_params.right_fq}'
                #end if
            #end if

            --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"

        #if str($params.settingsType) == "full":
            --min_junction_reads $params.min_junction_reads
            --min_sum_frags $params.min_sum_frags
            --max_promiscuity $params.max_promiscuity
            --min_novel_junction_support $params.min_novel_junction_support
            --min_alt_pct_junction $params.min_alt_pct_junction
            --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
            --E $params.E
        #end if
    ]]></command>

    <inputs>
        <conditional name="input_params">
            <param name="input_source"
                   type="select"
                   label="Use output from earlier STAR run or let STAR Fusion control running STAR">
                <option value="use_chimeric">Use output from earlier STAR</option>
                <option value="use_fastq">Let STAR Fusion control running STAR</option>
            </param>
            <when value="use_chimeric">
                <param name="chimeric_junction"
                       type="data"
                       format="interval"
                       argument="--chimeric_junction"
                       label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
            </when>
            <when value="use_fastq">
                <param name="left_fq"
                       type="data"
                       format="fastqsanger"
                       argument="--left_fq"
                       label="left.fq file"/>
                <param name="right_fq"
                       type="data"
                       format="fastqsanger"
                       optional="true"
                       argument="--right_fq"
                       label="right.fq file (actually optional, but highly recommended)"/>
            </when>
        </conditional>

        <!-- Genome source. -->
        <conditional name="fasta_type">
            <param name="fasta_type_selector" type="select" label="Source for sequence to search">
                <option value="cached">Locally Cached sequences</option>
                <option value="history" selected="true">Sequences from your history</option>
            </param>
            <when value="cached">
                <param name="ownFile"
                       type="select" label="Genome to search">
                    <options from_data_table="all_fasta">
                        <column name="value" index="3"/>
                        <column name="dbkey" index="1"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ownFile"
                       type="data"
                       format="fasta"
                       metadata_name="dbkey"
                       label="Select the reference genome (FASTA file)"/>
            </when>
        </conditional>
        
        <param name="geneModel"
               type="data"
               format="gff3,gtf"
               label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/>
        <param name="blast_pairs"
               type="data"
               format="tabular"
               label="Result of BLAST+-blastn of the reference fasta sequence with itself"
               help="Run blastn with '-outputfmt 6' or choose 'Tabular (standard 12 columns)' in the Galaxy wrapper. For human data it is recommended to obtain it from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/"/>
        
        <conditional name="params">
            <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR Fusion parameter.">
                <option value="default" selected="true">Use Defaults</option>
                <option value="full">Full parameter list</option>
            </param>
            <when value="default" />
            <when value="full"><!-- Full/advanced params. -->
                <param name="min_junction_reads"
                       type="integer" value="1"
                       label="minimum number of junction-spanning reads required."
                       argument="--min_junction_reads"/>
                <param name="min_sum_frags"
                       type="integer"
                       value="2"
                       label="minimum fusion support = (#junction_reads + #spanning_frags)"
                       argument="--min_sum_frags"/>
                <param name="max_promiscuity"
                       type="integer"
                       value="3"
                       label="maximum number of partners allowed for a given fusion"
                       argument="--max_promiscuity"/>
                <param name="min_novel_junction_support"
                       type="integer"
                       value="3"
                       label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions"
                       argument="--min_novel_junction_support"/>
                <param name="min_alt_pct_junction"
                       type="float"
                       value="10"
                       label="10% of the dominant isoform junction support"
                       argument="--min_alt_pct_junction"/>
                <param name="aggregate_novel_junction_dist"
                       type="integer"
                       value="5"
                       label="non-ref junctions within 5 are merged into single calls"
                       argument="--aggregate_novel_junction_dist"/>
                <param name="E"
                       type="float"
                       value="0.001"
                       label="E-value threshold for blast searches"
                       argument="-E"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>
    </outputs>

    <tests>
        <test>
            <param name="input_source" value="use_chimeric" />
            <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
            <param name="fasta_type_selector" value="history" />
            <param name="ownFile" ftype="fasta" value="test1.fa" />
            <param name="geneModel" ftype="gtf" value="test1.gtf" />
            <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
            <param name="settingsType" value="default" />
            
            <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
            <output name="output_final">
                <assert_contents>
                    <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
                    <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_source" value="use_fastq" />
            <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
            <param name="fasta_type_selector" value="history" />
            <param name="ownFile" ftype="fasta" value="test1.fa" />
            <param name="geneModel" ftype="gtf" value="test1.gtf" />
            <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
            <param name="settingsType" value="default" />
            
            <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
            <output name="output_final">
                <assert_contents>
                    <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
                    <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        **What it does**
        
        STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
        
        **Input**
        
        A reference genome and corresponding protein-coding gene annotation set, including blast-matching gene pairs must be provided to STAR-Fusion.
        
         We provide several alternative resources for human fusion transcript detection depending on whether you want to use GRCh37 or GRCh38 reference human genomes and corresponding Gencode annotation sets. Options are available here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/, so choose one. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.

        In Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

        More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki

    </help>

    <citations>
        <citation type="bibtex">
           @unpublished{star_fusion,
              author = {Brian Haas and Nicolas Stransky and Daniel Nicorici}, 
              title  = {STAR-Fusion},
              url    = {https://github.com/STAR-Fusion/STAR-Fusion}
            }
        </citation>
    </citations>
</tool>