comparison arriba.xml @ 7:25d207f7ff83 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"

6:7253b367c082

    #if $input_params.chimeric
        -c '$input_params.chimeric'
    #end if
#end if
    -a '$genome_assembly'
    -g '$gtf'
    #if $blacklist
        -b '$blacklist'
    #else
        -f 'blacklist'
    #end if

#elif str($visualization.do_viz) == "yes"
    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if str($visualization.do_viz) == "yes"
&& draw_fusions.R 
    --fusions=fusions.tsv 
    --alignments=Aligned.sortedByCoord.out.bam 
    --annotation='$gtf'
    --output=fusions.pdf 
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if $protein_domains
    --proteinDomains='$protein_domains'
    #end if
    ## Visualization Options
    #if $visualization.options.transcriptSelection
        --transcriptSelection=$visualization.options.transcriptSelection
    #end if
    #if $visualization.options.minConfidenceForCircosPlot
        --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
    #end if
    #if $visualization.options.showIntergenicVicinity
        --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
    #end if
    #if $visualization.options.squishIntrons
        --squishIntrons=$visualization.options.squishIntrons
    #end if
    #if $visualization.options.mergeDomainsOverlappingBy
        --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
    #end if
    #if $visualization.options.printExonLabels
        --printExonLabels=$visualization.options.printExonLabels
    #end if
    #if $visualization.options.render3dEffect
        --render3dEffect=$visualization.options.render3dEffect
    #end if
    #if $visualization.options.optimizeDomainColors
        --optimizeDomainColors=$visualization.options.optimizeDomainColors
    #end if
    #if $visualization.options.color1
        --color1=$visualization.options.color1
    #end if
    #if $visualization.options.color2
        --color2=$visualization.options.color2
    #end if
    #if $visualization.options.pdfWidth
        --pdfWidth=$visualization.options.pdfWidth
    #end if
    #if $visualization.options.pdfHeight
        --pdfHeight=$visualization.options.pdfHeight
    #end if
    #if $visualization.options.fontSize
        --fontSize=$visualization.options.fontSize
    #end if
#end if
    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">

                    </when> 
                </conditional>
            </when>
        </conditional>
        <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
        <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
        <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>
        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
        <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz"  optional="true" label="File containing known fusions">
            <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
        </param>

            <param name="do_viz" type="select" label="Generate visualization">
                <option value="yes">Yes</option>
                <option value="no">no</option>
            </param>
            <when value="yes">
                <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                <section name="options" expanded="false" title="Visualization Options">
                    <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
                        <help>By default the transcript isoform with the highest coverage is drawn. 
                             Alternatively, the transcript isoform that is provided in the columns 
                             transcript_id1 and transcript_id2 in the given fusions file can be drawn. 
                             Selecting the isoform with the highest coverage usually produces nicer plots, 
                             in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint. 
                             However, the isoform with the highest coverage may not be the one that is involved in the fusion. 
                             Often, genomic rearrangements lead to non-canonical isoforms being transcribed. 
                             For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2, 
                             which reflect the actual isoforms involved in a fusion. 
\                            As a third option, the transcripts that are annotated as canonical can be drawn. 
                             Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
                        </help>
                        <option value="coverage">coverage</option>
                        <option value="provided">provided</option>
                        <option value="canonical">canonical</option>
                    </param>
                    <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
                        <help>The fusion of interest is drawn as a solid line in the circos plot. 
                              To give an impression of the overall degree of rearrangement, 
                              all other fusions are drawn as semi-transparent lines in the background. 
                              This option determines which other fusions should be included in the circos plot. 
                              Values specify the minimum confidence a fusion must have to be included. 
                              It usually makes no sense to include low-confidence fusions in circos plots, 
                              because they are abundant and unreliable, and would clutter up the circos plot.
                              Default: medium
                        </help>
                        <option value="none">none - only the fusion of interest is drawn</option>
                        <option value="low">low</option>
                        <option value="medium">medium</option>
                        <option value="high">high</option>
                    </param>
                    <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">
                        <help>This option only applies to intergenic breakpoints. 
                              If it is set to a value greater than 0, then the script draws the genes
                              which are no more than the given distance away from an intergenic breakpoint. 
                              Note that this option is incompatible with squishIntrons. 
                              Default: 0
                        </help>
                    </param>
                    <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
                        <help>Exons usually make up only a small fraction of a gene. 
                              They may be hard to see in the plot. i
                              Since introns are in most situations of no interest in the context of gene fusions, 
                              this switch can be used to shrink the size of introns to a fixed, negligible size. 
                              It makes sense to disable this feature, if breakpoints in introns are of importance. 
                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>

                    <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
                        <help>Occasionally, domains are annotated redundantly. 
                              For example, tyrosine kinase domains are frequently annotated as 
                              Protein tyrosine kinase and Protein kinase domain. 
                              In order to simplify the visualization, such domains can be merged into one, 
                              given that they overlap by the given fraction. 
                              The description of the larger domain is used. 
                              Default: 0.9
                        </help>
                    </param>
                    <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
                        <help>By default the number of an exon is printed inside each exon, 
                              which is taken from the attribute exon_number of the GTF annotation. 
                              When a gene has many exons, the boxes may be too narrow to contain the labels, 
                              resulting in unreadable exon labels. In these situations, i
                              it may be better to turn off exon labels. 
                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
                        <help>Whether light and shadow should be rendered to give objects a 3D effect. 
                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
                        <help>By default, the script colorizes domains according to the colors 
                              specified in the file given in --annotation. 
                              This way, coloring of domains is consistent across all proteins. 
                              But since there are more distinct domains than colors, 
                              this can lead to different domains having the same color. 
                              If this option is set to TRUE, the colors are recomputed for each fusion separately. 
                              This ensures that the colors have the maximum distance for each individual fusion, 
                              but they are no longer consistent across different fusions. 
                              Default: FALSE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--color1" type="color" value="" optional="true"  label="Color of the 5' end of the fusion."/>
                    <param argument="--color2" type="color" value="" optional="true"  label="Color of the 3' end of the fusion."/>
                    <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
                           help="Default: 11.692"/>
                    <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
                           help="Default: 8.267"/>
                    <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
                           help="Default: 1.0"/>
                </section>

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

    </inputs>
    <outputs>
        <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
        <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
            <filter> output_fusions_discarded == "yes"</filter>
        </data> 
        <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
            <filter>input_params['input_source'] == "use_fastq"</filter>
        </data> 

            <conditional name="input_params">
                <param name="input_source" value="use_star"/>
                <param name="input" ftype="sam" value="Aligned.out.sam"/>
            </conditional>
            <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
            <param name="gtf" ftype="gtf" value="genome.gtf"/>
            <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
            <conditional name="visualization">
                <param name="do_viz" value="no"/>
                <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
            </conditional>
            <output name="fusions">
                <assert_contents>
                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
        </test>

            <conditional name="input_params">
                <param name="input_source" value="use_star"/>
                <param name="input" ftype="sam" value="Aligned.out.sam"/>
            </conditional>
            <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
            <param name="gtf" ftype="gtf" value="genome.gtf"/>
            <conditional name="visualization">
                <param name="do_viz" value="yes"/>
            </conditional>
            <output name="fusions">
                <assert_contents>
                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
        </test>

    </tests>

7:25d207f7ff83

    #if $input_params.chimeric
        -c '$input_params.chimeric'
    #end if
#end if
    -a '$genome_assembly'
    -g '$annotation'
    #if $blacklist
        -b '$blacklist'
    #else
        -f 'blacklist'
    #end if

#elif str($visualization.do_viz) == "yes"
    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if str($visualization.do_viz) == "yes"
#set $fusions = 'fusions.tsv'
&& @DRAW_FUSIONS@
#end if
    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">

                    </when> 
                </conditional>
            </when>
        </conditional>
        <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
        <param name="annotation" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
        <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>
        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
        <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz"  optional="true" label="File containing known fusions">
            <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
        </param>

            <param name="do_viz" type="select" label="Generate visualization">
                <option value="yes">Yes</option>
                <option value="no">no</option>
            </param>
            <when value="yes">
                <expand macro="visualization_options" />
            </when>
            <when value="no"/>
        </conditional>

    </inputs>
    <outputs>
        <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
        <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
            <filter> output_fusions_discarded == "yes"</filter>
        </data> 
        <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
            <filter>input_params['input_source'] == "use_fastq"</filter>
        </data> 

            <conditional name="input_params">
                <param name="input_source" value="use_star"/>
                <param name="input" ftype="sam" value="Aligned.out.sam"/>
            </conditional>
            <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
            <param name="annotation" ftype="gtf" value="genome.gtf"/>
            <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
            <conditional name="visualization">
                <param name="do_viz" value="no"/>
                <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
            </conditional>
            <output name="fusions_tsv">
                <assert_contents>
                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
        </test>

            <conditional name="input_params">
                <param name="input_source" value="use_star"/>
                <param name="input" ftype="sam" value="Aligned.out.sam"/>
            </conditional>
            <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
            <param name="annotation" ftype="gtf" value="genome.gtf"/>
            <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
            <conditional name="visualization">
                <param name="do_viz" value="yes"/>
                <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
            </conditional>
            <output name="fusions_tsv">
                <assert_contents>
                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
            <output name="fusions_pdf">
                <assert_contents>
                    <has_size value= "64000" delta="5000" />
                </assert_contents>
            </output>
        </test>

    </tests>