comparison rg_rnaStar.xml @ 15:5ec75f5dae3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"

14:b9e04854e2bb

                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
            </when>
        </conditional>

        <!-- Genome source. -->
        <expand macro="refgenomehandling" />

        <conditional name="twopass">
            <param argument="--twopassMode" type="select"
            label="Use 2-pass mapping for more sensitive novel splice junction discovery"
            help="For a study with multiple samples, multisample 2-pass mapping is the most sensitive approach. It involves two separate runs of STAR for each sample, where, in the second run of each sample, the splice junctions found in any sample in the first runs are treated as additional known junctions. If you plan to use the mapping results as input for STAR-Fusion it is recommended that you use at least single-sample 2-pass mapping of all reads.">

15:5ec75f5dae3c

                <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
            </when>
        </conditional>

        <!-- Genome source. -->
        <conditional name="refGenomeSource">
            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
                <option value="indexed" selected="true">Use a built-in index</option>
                <option value="history">Use reference genome from history and create temporary index</option>
            </param>
            <when value="indexed">
                <conditional name="GTFconditional">
                    <param name="GTFselect" type="select"
                           label="Reference genome with or without an annotation"
                           help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations.">
                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="index_selection" with_gene_model="1" />
                    </when>
                    <when value="without-gtf">
                        <expand macro="index_selection" with_gene_model="0" />
                        <expand macro="@SJDBOPTIONS@" />
                    </when>
                </conditional>
            </when>
            <when value="history">
                <expand macro="ref_selection" />
                <conditional name="GTFconditional">
                    <param name="GTFselect" type="select"
                           label="Build index with or without known splice junctions annotation"
                           help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
                        <option value="without-gtf">build index without gene-model</option>
                        <option value="with-gtf">build index with gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <expand macro="@SJDBOPTIONS@" optional="false"/>
                    </when>
                    <when value="without-gtf" />
                </conditional>
            </when>
        </conditional>

        <conditional name="twopass">
            <param argument="--twopassMode" type="select"
            label="Use 2-pass mapping for more sensitive novel splice junction discovery"
            help="For a study with multiple samples, multisample 2-pass mapping is the most sensitive approach. It involves two separate runs of STAR for each sample, where, in the second run of each sample, the splice junctions found in any sample in the first runs are treated as additional known junctions. If you plan to use the mapping results as input for STAR-Fusion it is recommended that you use at least single-sample 2-pass mapping of all reads.">