comparison salmon.xml @ 6:aa4332ee7d1d draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7fae9d149b8b6aab2d01d94f137efc2967c7ee7

5:83bbe4e20bdc

            help=""/>
        <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
            label="Perform fragment GC bias correction"
            help=""/>
        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
            label="File containing a mapping of transcripts to genes.  If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
        <section name="adv" title="Additional Options">
            <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
                label="Write Mappings"
                help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"

6:aa4332ee7d1d

            help=""/>
        <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
            label="Perform fragment GC bias correction"
            help=""/>
        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
            label="File containing a mapping of transcripts to genes" 
            help="If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
        <section name="adv" title="Additional Options">
            <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
                label="Write Mappings"
                help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"