comparison macros.xml @ 2:2aad7301632d draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34

1:0e25453fbee7

<macros>
    <token name="@TOOL_VERSION@">1.2.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement>
            <yield/>

                <option value="no">No - use default options</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="-percolatorVersionNumber" type="integer" value="3" min="2" max="3" label="percolatorVersionNumber"/>
                <param argument="-percolatorProteinThreshold" type="float" value="0.01" label="percolatorProteinThreshold"/>
                <param argument="-percolatorThreshold" type="float" value="0.01" label="percolatorThreshold"/>
            </when>
        </conditional>
    </xml>
    <token name="@PERCOLATOR_OPTIONS@">
    #if $options.percolator.set_percolator == 'yes'
        #if str($options.percolator.percolatorVersionNumber)
            -percolatorVersionNumber $options.percolator.percolatorVersionNumber
        #end if
        #if str($options.percolator.percolatorProteinThreshold)
            -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
        #end if
        #if str($options.percolator.percolatorThreshold)
            -percolatorThreshold $options.percolator.percolatorThreshold
        #end if
    #end if
    </token>

    <xml name="peak_options">
        <conditional name="peak">

        #end if
        @SCAN_INPUTS@
        @FASTA_INPUT@
        @TARGET_FASTA@
        @LIB_INPUT@
        -a $a
        -o chromatogram_library.elib
        && ls -l ./*.* inputs/*
        | tee -a search2lib.log
]]>

2:2aad7301632d

<macros>
    <token name="@TOOL_VERSION@">1.12.34</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">encyclopedia</requirement>
            <yield/>

                <option value="no">No - use default options</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="-percolatorVersion" type="text" value="3.01" optional="true" label="percolatorVersion">
                     <option value="2.10">2.10</option>
                     <option value="3.01">3.01</option>
                     <option value="3.05">3.05</option>
                     <validator type="regex" message="Not percolator version format">^\d([.]\d+)?$</validator>
                </param>
                <param argument="-percolatorProteinThreshold" type="float" value="0.01" optional="true" label="percolatorProteinThreshold"/>
                <param argument="-percolatorThreshold" type="float" value="0.01" optional="true" label="percolatorThreshold"/>
            </when>
        </conditional>
    </xml>
    <token name="@PERCOLATOR_OPTIONS@">
    #if $options.percolator.set_percolator == 'yes'
        #if str($options.percolator.percolatorVersion)
            -percolatorVersion $options.percolator.percolatorVersion
        #end if
        #if str($options.percolator.percolatorProteinThreshold)
            -percolatorProteinThreshold $options.percolator.percolatorProteinThreshold
        #end if
        #if str($options.percolator.percolatorThreshold)
            -percolatorThreshold $options.percolator.percolatorThreshold
        #end if
    #else 
        -percolatorVersion "3.01"
    #end if
    </token>

    <xml name="peak_options">
        <conditional name="peak">

        #end if
        @SCAN_INPUTS@
        @FASTA_INPUT@
        @TARGET_FASTA@
        @LIB_INPUT@
        @MASS_LIBRARY_TOLERANCE@
        @PERCOLATOR_OPTIONS@
        @PEAK_OPTIONS@
        @WINDOW_OPTIONS@
        @MODIFICATION_OPTIONS@
        @SEARCH_OPTIONS@
        -a $a
        -o chromatogram_library.elib
        && ls -l ./*.* inputs/*
        | tee -a search2lib.log
]]>