comparison macros.xml @ 12:f2000bc73102 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664

11:e661a3269313

<macros>
    <token name="@TOOL_VERSION@">1.9.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>

                <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is 
                provided, then the output SAM file will contain quality strings as well as read sequences." />
            </when>
            <when value=""/>
        </conditional>
        <param name="writeMappings" type="boolean" truevalue="" falsevalue="" checked="False"
            label="Write Mappings to Bam File"
            help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format.  By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
        <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
        label="Consistent Hits"
        help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
        <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
        help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
    </xml>

12:f2000bc73102

<macros>
    <token name="@TOOL_VERSION@">1.9.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@IDX_VERSION@">q7</token>
    <token name="@PROFILE_VERSION@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>

                <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is 
                provided, then the output SAM file will contain quality strings as well as read sequences." />
            </when>
            <when value=""/>
        </conditional>
       <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
        label="Consistent Hits"
        help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
        <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
        help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
    </xml>