comparison star_fusion.xml @ 1:0b44456754e2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit d6a7537117d814677113ba9a8e4783a80dd228a2

0:93704f98f56e

<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>

            --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"

                       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>

            </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"

                    <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.

1:0b44456754e2

<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-3" profile="17.01">
    <description>detect fusion genes in RNA-Seq data</description>
    <requirements>
        <!-- Bio-conda -->
        <requirement type="package" version="0.5.4">star-fusion</requirement>
    </requirements>

            --gtf '${geneModel}'
            --blast_pairs "${blast_pairs}\$gzip_suffix"
            --CPU \${GALAXY_SLOTS:-1}
            --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
        &&

        ## 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"

                       label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
            </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)"/>
            </when>
        </conditional>

            </when>
            <when value="history">
                <param name="ownFile"
                       type="data"
                       format="fasta"
                       label="Select the reference genome (FASTA file)"/>
            </when>
        </conditional>
        
        <param name="geneModel"

                    <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.