comparison macros.xml @ 6:d25273689e04 draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"

5:50409aeeeac5

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.12.2</token>
    <token name="@GALAXY_TOOL_VERSION@">3</token>

    <xml name="requirements">
        <requirements>
           <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
           <requirement type="package" version="1.42.0" >bioconductor-camera</requirement>
           <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement>
           <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement>
           <requirement type="package" version="1.6.4">r-optparse</requirement>
           <requirement type="package" version="1.1.1">r-rpostgres</requirement>
           <requirement type="package" version="0.10.17">r-rmysql</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="text-adduct-regex-validator">

    </xml>

    <xml name="offsets">
        <param argument="--minoffset" type="float" label="minoffset" value="0.5"
               help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
               100.0 then the range would be from 999.5 to 100.0"/>
        <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
               help="Offset to the 'right' for the precursor range  e.g. if precursor of interest is
               100.0 then the range would be from 100.0 to 100.5"/>
    </xml>
    <xml name="general_params">
        <param argument="--ilim" type="float" value="0.05" 
               label="Threshold to remove peaks below x % of the relative intensity of
               precursor of interest"
               help="All peaks less than this percentage of the precursor ion of interest will be
               removed from the purity calculation, default is 5\% (0.05).
               Essentially a noise filter to remove peaks that are thought to have either none or

                <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
                help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true"  label="Spectra type" >
                        <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
                        <option value="av_inter">Averaged inter spectra</option>
                        <option value="av_intra">Averaged intra spectra </option>
                        <option value="scans">All individual scans</option>
                        <option value="NA">Not applicable/defined</option>
                    </param>
                </when>
                <when value="false">

6:d25273689e04

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.16.2</token>
    <token name="@GALAXY_TOOL_VERSION@">0</token>

    <xml name="requirements">
        <requirements>
           <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
           <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
           <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
           <requirement type="package" version="1.16.0" >bioconductor-mspuritydata</requirement>
           <requirement type="package" version="1.6.6">r-optparse</requirement>
           <requirement type="package" version="1.3.1">r-rpostgres</requirement>
           <requirement type="package" version="0.10.21">r-rmysql</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="text-adduct-regex-validator">

    </xml>

    <xml name="offsets">
        <param argument="--minoffset" type="float" label="minoffset" value="0.5"
               help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
               100.0 then the range would be from 99.5 to 100.0"/>
        <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
               help="Offset to the 'right' for the precursor range  e.g. if precursor of interest is
               100.0 then the range would be from 100.0 to 100.5"/>
    </xml>
    <xml name="general_params">
        <param argument="--ilim" type="float" value="0.05"
               label="Threshold to remove peaks below x % of the relative intensity of
               precursor of interest"
               help="All peaks less than this percentage of the precursor ion of interest will be
               removed from the purity calculation, default is 5\% (0.05).
               Essentially a noise filter to remove peaks that are thought to have either none or

                <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
                help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true"  label="Spectra type" >
                        <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
                        <option value="inter">Averaged inter spectra</option>
                        <option value="intra">Averaged intra spectra </option>
                        <option value="scans">All individual scans</option>
                        <option value="NA">Not applicable/defined</option>
                    </param>
                </when>
                <when value="false">