comparison macros.xml @ 15:97a7f34fcb6a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"

14:e42225f8a659

<?xml version="1.0" ?>
<macros>
    <token name="@VERSION@">1.6.17.0</token>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@VERSION_PTXQC@">1.0.10</token>
    <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
    <token name="@TMT2PLEX@">
                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]

                    - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True]
                    - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True]
                    - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True]
                    - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True]
                    - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True]
    </token>
    <token name="@ITRAQ4PLEX@">
                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]

                PeptideCountThresh_num: 15000.0
                SpecialContaminants:
                  cont_MYCO:
                  - MYCOPLASMA
                  - '1'
                #if $search_opts.mbr.match_between_runs == 'True':
                MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window}
                #else:
                MQpar_MatchingTimeWindow_num: 0.0
                #end if
                MatchBetweenRuns_wA: auto
                MQpar_firstSearchTol_num: 20.0
                firstSearch_outOfCalWarnSD_num: 2.0
                MQpar_mainSearchTol_num: 4.5
              MsMs:

        <expand macro="mod_option" value="TMTpro16plex-Lys132N"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys132C"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys133N"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys133C"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys134N"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @article{cox2008maxquant,

15:97a7f34fcb6a

<?xml version="1.0" ?>
<macros>
    <token name="@VERSION@">1.6.17.0</token>
    <token name="@VERSION_SUFFIX@">3</token>
    <token name="@VERSION_SUFFIX_MQPAR@">0</token>
    <token name="@VERSION_PTXQC@">1.0.10</token>
    <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
    <token name="@TMT2PLEX@">
                    - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
                    - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]

                    - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True]
                    - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True]
                    - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True]
                    - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True]
                    - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True]
    </token>
    <token name="@TMTPRO18PLEX@">
                    @TMTPRO16PLEX@
                    - [TMTpro18plex-Lys134C,TMTpro18plex-Nter134C,0,0,0,0,True]
                    - [TMTpro18plex-Lys135N,TMTpro18plex-Nter135N,0,0,0,0,True]
    </token>
    <token name="@ITRAQ4PLEX@">
                    - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
                    - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
                    - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]

                PeptideCountThresh_num: 15000.0
                SpecialContaminants:
                  cont_MYCO:
                  - MYCOPLASMA
                  - '1'
            #if $varExists("mqpar_input"):
                #import re
                #set $mqpar_xml = open(str($mqpar_input), "r").read()
                #set $matchingTimeWindow = re.search("matchingTimeWindow>(.*)./matchingTimeWindow", $mqpar_xml).group(1)
                MQpar_MatchingTimeWindow_num: ${matchingTimeWindow}
            #else:
                #if $search_opts.mbr.match_between_runs == 'True':
                MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window}
                #else:
                MQpar_MatchingTimeWindow_num: 0.0
                #end if
            #end if
                MatchBetweenRuns_wA: auto
                MQpar_firstSearchTol_num: 20.0
                firstSearch_outOfCalWarnSD_num: 2.0
                MQpar_mainSearchTol_num: 4.5
              MsMs:

        <expand macro="mod_option" value="TMTpro16plex-Lys132N"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys132C"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys133N"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys133C"/>
        <expand macro="mod_option" value="TMTpro16plex-Lys134N"/>
        <expand macro="mod_option" value="TMTpro18plex-Nter134C"/>
        <expand macro="mod_option" value="TMTpro18plex-Nter135N"/>
        <expand macro="mod_option" value="TMTpro18plex-Lys134C"/>
        <expand macro="mod_option" value="TMTpro18plex-Lys135N"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @article{cox2008maxquant,