comparison salmon.xml @ 5:53e9709776a0 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

4:570e7e9c19a5

                --fldSD $adv.fldSD
            #end if
            #if $adv.forgettingFactor:
                --forgettingFactor $adv.forgettingFactor
            #end if
            $adv.writeMappings
            #if str($adv.maxOcc):
                --maxOcc $adv.maxOcc
            #end if
            $adv.initUniform
            $adv.noFragLengthDist

            $adv.perTranscriptPrior
            #if $adv.vbPrior:
                --vbPrior $adv.vbPrior
            #end if
            $adv.writeUnmappedNames
]]>
    </command>

    <inputs>
        <conditional name="refTranscriptSource">

            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"
                label="Incompatible Prior"
                help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
            <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
                label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>

    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
            <filter>geneMap</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="single_or_paired_opts" value="paired" />

5:53e9709776a0

                --fldSD $adv.fldSD
            #end if
            #if $adv.forgettingFactor:
                --forgettingFactor $adv.forgettingFactor
            #end if
            #if str($adv.maxOcc):
                --maxOcc $adv.maxOcc
            #end if
            $adv.initUniform
            $adv.noFragLengthDist

            $adv.perTranscriptPrior
            #if $adv.vbPrior:
                --vbPrior $adv.vbPrior
            #end if
            $adv.writeUnmappedNames
            #if str($adv.writeMappings):
                $adv.writeMappings > ${output_sam}
            #end if
]]>
    </command>

    <inputs>
        <conditional name="refTranscriptSource">

            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="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
                label="Incompatible Prior"
                help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
            <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
                label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>

    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
            <filter>geneMap</filter>
        </data>
        <data name="output_sam" format="sam" label="${tool.name} on ${on_string} (SAM format)">
            <filter>adv['writeMappings']</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="single_or_paired_opts" value="paired" />