comparison arriba.xml @ 2:7420753b0671 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"

1:9f2665b32c45

        #set read2 = 'input_2.fastq.gz'
    #else:
        #set read2 = 'input_2.fastq'
    #end if
    ln -f -s '${input_params.right_fq}' ${read2} &&
    STAR 
    --runThreadN \${GALAXY_SLOTS:-1} 
    --genomeDir /path/to/STAR_index 
    --genomeLoad NoSharedMemory 
    --readFilesIn $read1 $read2
    --readFilesCommand zcat 
    --outStd BAM_Unsorted 
    --outSAMtype BAM Unsorted 

    -o fusions.tsv
    -O fusions.discarded.tsv 
    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source"
                   type="select"
                   label="Use output from earlier STAR run or let Arriba running STAR">
                <option value="use_star">Use output from earlier STAR</option>
                <option value="use_fastq">Let Arriba control running STAR</option>
            </param>
            <when value="use_star">
                <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/>

                <param name="right_fq"
                       type="data"
                       format="fastqsanger,fastqsanger.gz"
                       argument="--right_fq"
                       label="right.fq file"/>
            </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" label="File containing blacklisted ranges."/>

    The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
      * Name=PROTEIN_DOMAIN_NAME;
      * gene_id=GENE_ID;
      * gene_name=GENE_NAME
    The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.

  - Structural variant calls from WGS

    If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects:

2:7420753b0671

        #set read2 = 'input_2.fastq.gz'
    #else:
        #set read2 = 'input_2.fastq'
    #end if
    ln -f -s '${input_params.right_fq}' ${read2} &&
    #if str($input_params.index.index_source) == "history"
        #set $star_index_dir = $input_params.index.star_index.files_path
    #end if
    STAR 
    --runThreadN \${GALAXY_SLOTS:-1} 
    --genomeDir $star_index_dir
    --genomeLoad NoSharedMemory 
    --readFilesIn $read1 $read2
    --readFilesCommand zcat 
    --outStd BAM_Unsorted 
    --outSAMtype BAM Unsorted 

    -o fusions.tsv
    -O fusions.discarded.tsv 
    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
                <option value="use_star">Use output from earlier STAR</option>
                <option value="use_fastq">Let Arriba control running STAR</option>
            </param>
            <when value="use_star">
                <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/>

                <param name="right_fq"
                       type="data"
                       format="fastqsanger,fastqsanger.gz"
                       argument="--right_fq"
                       label="right.fq file"/>
                <conditional name="index">
                    <param name="index_source" type="select" label="Arriba STAR index source">
                        <option value="history">Arriba STAR index from your history</option>
                    </param>
                    <when value="history">
                        <param name="star_index" argument="--genomeDir" type="data" format="txt" label="Arriba STAR index"
                            help="generated by:  Arriba Reference"/>
                    </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" label="File containing blacklisted ranges."/>

    The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
      * Name=PROTEIN_DOMAIN_NAME;
      * gene_id=GENE_ID;
      * gene_name=GENE_NAME

    The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.

  - Structural variant calls from WGS

    If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects: