comparison macros.xml @ 32:ff592231f118 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d

31:f3f67aa3123b

            -prec_ppm "${precursor_ion_tol_units}"
            ### -digestion
            ### multiple enzymes?
            -enzyme "${enzyme}"
            ### -specificity
            #set $fixed_mods_str = $fixed_modifications or ''
            #set $variable_mods_str = $variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "$fixed_mods_str" 
            #end if
            #if $variable_mods_str
                -variable_mods "$variable_mods_str"
            #end if
            -min_charge $min_charge
            -max_charge $max_charge
            ### value per enzyme
            -mc $missed_cleavages
            -fi $forward_ion
            -ri $reverse_ion
    </token>
    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
    <token name="@SEARCHGUI_VERSION@">3.1.4</token>
    <xml name="general_options">
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"

        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
            <option value="x">x</option>
            <option value="y" selected="true">y</option>
            <option value="z">z</option>
        </param>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/1471-2105-12-70</citation>

32:ff592231f118

            -prec_ppm "${precursor_ion_tol_units}"
            ### -digestion
            ### multiple enzymes?
            -enzyme "${enzyme}"
            ### -specificity
            ### value per enzyme
            -mc $missed_cleavages
            #set $fixed_mods_str = $fixed_modifications or ''
            #set $variable_mods_str = $variable_modifications or ''
            #if $fixed_mods_str
                -fixed_mods "$fixed_mods_str" 
            #end if
            #if $variable_mods_str
                -variable_mods "$variable_mods_str"
            #end if
            -min_charge $min_charge
            -max_charge $max_charge
            -fi $forward_ion
            -ri $reverse_ion
            -min_isotope ${min_isotope} 
            -max_isotope ${max_isotope} 

    </token>
    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
    <token name="@SEARCHGUI_VERSION@">3.1.4</token>
    <xml name="general_options">
        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"

        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
            <option value="x">x</option>
            <option value="y" selected="true">y</option>
            <option value="z">z</option>
        </param>
        <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
        <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/1471-2105-12-70</citation>