comparison rg_rnaStarSolo.xml @ 12:79b885ce78d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb

11:eec9494fdafa

<tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT">
    <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
    <xrefs>
        <xref type="bio.tools">star</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="edam"/>
    <expand macro="stdio" >
        <regex match="Segmentation fault" source="both" level="fatal" />
    </expand>

    <command><![CDATA[

                <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 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">

                </param>
            </when>
        </conditional>
        <section name="solo" title="Advanced Settings" expanded="true">
            <param argument="--soloStrand" type="select" label="Strandedness of Library" help="Unstranded has no strand information, Forward has the read strand the same as the original RNA molecule, Reverse has the read strand opposite to the original RNA molecule">
                <option value="Unstranded" />
                <option value="Forward" selected="true" />
                <option value="Reverse" />
            </param>
            <param argument="--soloFeatures" type="select" label="Collect UMI counts for these genomic features" >
                <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option>
                <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option>
                <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>

12:79b885ce78d7

<tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT">
    <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam"/>
    <xrefs>
        <xref type="bio.tools">star</xref>
    </xrefs>
    <expand macro="requirements"/>
    <expand macro="stdio" >
        <regex match="Segmentation fault" source="both" level="fatal" />
    </expand>

    <command><![CDATA[

                <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 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 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">

                </param>
            </when>
        </conditional>
        <section name="solo" title="Advanced Settings" expanded="true">
            <param argument="--soloStrand" type="select" label="Strandedness of Library" help="Unstranded has no strand information, Forward has the read strand the same as the original RNA molecule, Reverse has the read strand opposite to the original RNA molecule">
                <option value="Unstranded" >No strand information</option>
                <option value="Forward" selected="true" >Read strand same as the original RNA molecule</option>
                <option value="Reverse" >Read strand opposite to the original RNA molecule</option>
            </param>
            <param argument="--soloFeatures" type="select" label="Collect UMI counts for these genomic features" >
                <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option>
                <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option>
                <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option>