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comparison salmon.xml @ 4:570e7e9c19a5 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7fae9d149b8b6aab2d01d94f137efc2967c7ee7
author bgruening
date Fri, 30 Jun 2017 05:45:09 -0400
parents 5a60f347f566
children 53e9709776a0
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3:5a60f347f566 4:570e7e9c19a5
232 help=""/> 232 help=""/>
233 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False" 233 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
234 label="Perform fragment GC bias correction" 234 label="Perform fragment GC bias correction"
235 help=""/> 235 help=""/>
236 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" 236 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
237 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." /> 237 label="File containing a mapping of transcripts to genes"
238 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." />
238 <section name="adv" title="Additional Options"> 239 <section name="adv" title="Additional Options">
239 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False" 240 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
240 label="Write Mappings" 241 label="Write Mappings"
241 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." /> 242 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." />
242 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21" 243 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"