comparison star_fusion.xml @ 0:5ff7593a7220 draft

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0:5ff7593a7220

<tool id="star_fusion" name="STAR-Fusion" version="1.1.0" profile="17.01">
    <description>detect fusion genes in RNA-Seq data</description>
    <requirements>
        <!-- Bio-conda -->
        <requirement type="package" version="1.1.0">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[
        #if reference.reference_type_selector == 'cached':
            ln -s '$reference.ctat_resource_lib'  tmp_star_fusion_genome_dir
        #else
            ## 1. ensure the blastn file is provided as *.gz
            if file --mime-type '${reference.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 -- '${reference.blast_pairs}' > '${reference.blast_pairs}.gz' &&
                gzip_suffix='.gz' ;
            fi &&
            
            ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
            ## - @todo once write a decent STAR and STAR Fusion data manager
            prep_genome_lib.pl
                --genome_fa '${reference.fasta_type.ownFile}'
                --gtf '${reference.geneModel}'
                --blast_pairs "${reference.blast_pairs}\$gzip_suffix"
                --CPU \${GALAXY_SLOTS:-1}
                --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
        #end if
        &&

        ## Link in fastq files so they have appropriate extensions
        #if str($input_params.input_source) != "use_chimeric":
            #if $input_params.left_fq.is_of_type("fastq.gz"):
                #set read1 = 'input_1.fastq.gz'
            #else:
                #set read1 = 'input_1.fastq'
            #end if
            ln -f -s '${input_params.left_fq}' ${read1} &&

            #if $input_params.right_fq:
                #if $input_params.right_fq.is_of_type("fastq.gz"):
                    #set read2 = 'input_2.fastq.gz'
                #else:
                    #set read2 = 'input_2.fastq'
                #end if
                ln -f -s '${input_params.right_fq}' ${read2} &&
            #end if
        #end if
        
        ## 3. Run STAR-Fusion
        STAR-Fusion
            #if str($input_params.input_source) == "use_chimeric":
                --chimeric_junction '${input_params.chimeric_junction}'
            #else:
                --left_fq ${read1}
                #if $input_params.right_fq:
                    --right_fq ${read2}
                #end if
            #end if

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

            str($input_params.optional_outputs).replace(',',' ')

        #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
        --CPU \${GALAXY_SLOTS:-1}
    ]]></command>

    <inputs>
        <conditional name="reference">
            <param name="reference_type_selector" type="select" label="Star Fusion Genome Reference Source">
                <option value="cached">Locally Cached sequences</option>
                <option value="build" selected="true">Sequences from your history</option>
            </param>
            <when value="cached">
                <param name="ctat_resource_lib" type="select" label="Genome to search">
                    <options from_data_table="ctat_resource">
                        <column name="dbkey" index="1"/>
                        <column name="name" index="2"/>
                        <column name="value" index="3"/>
                    </options>
                </param>
            </when>
            <when value="build">
                <!-- 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="dbkey" index="1"/>
                                <column name="name" index="2"/>
                                <column name="value" index="3"/>
                            </options>
                        </param>
                    </when>
                    <when value="history">
                        <param name="ownFile"
                               type="data"
                               format="fasta"
                               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/"/>
            </when>
        </conditional>
 

        <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)"/>
                 <param name="optional_outputs" type="select" multiple="true" label="Additional Outputs">
                     <option value="--annotate">--annotate</option>
                     <option value="--examine_coding_effect">--examine_coding_effect</option>
                 </param>
            </when>
            <when value="use_fastq">
                <param name="left_fq"
                       type="data"
                       format="fastqsanger,fastqsanger.gz"
                       argument="--left_fq"
                       label="left.fq file"/>
                <param name="right_fq"
                       type="data"
                       format="fastqsanger,fastqsanger.gz"
                       optional="true"
                       argument="--right_fq"
                       label="right.fq file (actually optional, but highly recommended)"/>
                 <param name="optional_outputs" type="select" multiple="true" label="Additional Outputs">
                     <option value="--annotate">--annotate</option>
                     <option value="--examine_coding_effect">--examine_coding_effect</option>
                     <option value="--extract_fusion_reads">--extract_fusion_reads</option>
                 </param>
            </when>
        </conditional>

        <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="bam" name="out_bam" label="${tool.name} on ${on_string}: Aligned.sortedByCoord.out.bam" from_work_dir="star-fusion.fusion_candidates.final"/>
        <data format="fastqsanger" name="output_reads_1" label="${tool.name} on ${on_string}: fusion_evidence_reads_1" from_work_dir="star-fusion.fusion_evidence_reads_1.fq">
            <filter>input_params['input_source'] == 'use_fastq' and str(input_params['optional_outputs']).find('extract_fusion_reads') > 0</filter>
        </data>
        <data format="fastqsanger" name="output_reads_2" label="${tool.name} on ${on_string}: fusion_evidence_reads_2" from_work_dir="star-fusion.fusion_evidence_reads_2.fq">
            <filter>input_params['input_source'] == 'use_fastq' and str(input_params['optional_outputs']).find('extract_fusion_reads') > 0</filter>
        </data>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_predictions.tsv" from_work_dir="star-fusion.fusion_predictions.tsv"/>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_predictions.abridged.tsv" from_work_dir="star-fusion.fusion_predictions.abridged.tsv"/>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_predictions.abridged.annotated.tsv" from_work_dir="star-fusion.fusion_predictions.abridged.annotated.tsv">
            <filter>str(input_params['optional_outputs']).find('annotate') > 0 and not str(input_params['optional_outputs']).find('examine_coding_effect') > 0</filter>
        </data>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_predictions.abridged.coding_effect.tsv" from_work_dir="star-fusion.fusion_predictions.abridged.coding_effect.tsv">
            <filter>str(input_params['optional_outputs']).find('examine_coding_effect') > 0 and not str(input_params['optional_outputs']).find('annotate') > 0</filter>
        </data>
        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_predictions.abridged.annotated.coding_effect.tsv" from_work_dir="star-fusion.fusion_predictions.abridged.annotated.coding_effect.tsv">
            <filter>str(input_params['optional_outputs']).find('annotate') > 0 and str(input_params['optional_outputs']).find('examine_coding_effect') > 0</filter>
        </data>
    </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>
        <test>
            <param name="input_source" value="use_fastq" />
            <param name="left_fq" ftype="fastqsanger.gz" value="test1.fastqsanger.gz"/>
            <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: files required to run STAR-Fusion**
 - A genome reference sequence (FASTA-format)
 - A corresponding protein-coding gene annotation set (GTF/GFF Format)
 - A last-matching gene pairs file - 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
 - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well.

The authors of STAR Fusion have made some of these files avaialble at: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.
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>