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comparison macros.xml @ 15:97a7f34fcb6a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
parents e42225f8a659
children 74f5d355d156
comparison
equal deleted inserted replaced
14:e42225f8a659 15:97a7f34fcb6a
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">1.6.17.0</token> 3 <token name="@VERSION@">1.6.17.0</token>
4 <token name="@VERSION_SUFFIX@">2</token> 4 <token name="@VERSION_SUFFIX@">3</token>
5 <token name="@VERSION_SUFFIX_MQPAR@">0</token>
5 <token name="@VERSION_PTXQC@">1.0.10</token> 6 <token name="@VERSION_PTXQC@">1.0.10</token>
6 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> 7 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
7 <token name="@TMT2PLEX@"> 8 <token name="@TMT2PLEX@">
8 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] 9 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
9 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] 10 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
57 - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True] 58 - [TMTpro16plex-Lys132C,TMTpro16plex-Nter132C,0,0,0,0,True]
58 - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True] 59 - [TMTpro16plex-Lys133N,TMTpro16plex-Nter133N,0,0,0,0,True]
59 - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True] 60 - [TMTpro16plex-Lys133C,TMTpro16plex-Nter133C,0,0,0,0,True]
60 - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True] 61 - [TMTpro16plex-Lys134N,TMTpro16plex-Nter134N,0,0,0,0,True]
61 - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True] 62 - [TMTpro16plex-Lys126C,TMTpro16plex-Nter126C,0,0,0,0,True]
63 </token>
64 <token name="@TMTPRO18PLEX@">
65 @TMTPRO16PLEX@
66 - [TMTpro18plex-Lys134C,TMTpro18plex-Nter134C,0,0,0,0,True]
67 - [TMTpro18plex-Lys135N,TMTpro18plex-Nter135N,0,0,0,0,True]
62 </token> 68 </token>
63 <token name="@ITRAQ4PLEX@"> 69 <token name="@ITRAQ4PLEX@">
64 - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False] 70 - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
65 - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False] 71 - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
66 - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False] 72 - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
129 PeptideCountThresh_num: 15000.0 135 PeptideCountThresh_num: 15000.0
130 SpecialContaminants: 136 SpecialContaminants:
131 cont_MYCO: 137 cont_MYCO:
132 - MYCOPLASMA 138 - MYCOPLASMA
133 - '1' 139 - '1'
140 #if $varExists("mqpar_input"):
141 #import re
142 #set $mqpar_xml = open(str($mqpar_input), "r").read()
143 #set $matchingTimeWindow = re.search("matchingTimeWindow>(.*)./matchingTimeWindow", $mqpar_xml).group(1)
144 MQpar_MatchingTimeWindow_num: ${matchingTimeWindow}
145 #else:
134 #if $search_opts.mbr.match_between_runs == 'True': 146 #if $search_opts.mbr.match_between_runs == 'True':
135 MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window} 147 MQpar_MatchingTimeWindow_num: ${search_opts.mbr.matching_time_window}
136 #else: 148 #else:
137 MQpar_MatchingTimeWindow_num: 0.0 149 MQpar_MatchingTimeWindow_num: 0.0
138 #end if 150 #end if
151 #end if
139 MatchBetweenRuns_wA: auto 152 MatchBetweenRuns_wA: auto
140 MQpar_firstSearchTol_num: 20.0 153 MQpar_firstSearchTol_num: 20.0
141 firstSearch_outOfCalWarnSD_num: 2.0 154 firstSearch_outOfCalWarnSD_num: 2.0
142 MQpar_mainSearchTol_num: 4.5 155 MQpar_mainSearchTol_num: 4.5
143 MsMs: 156 MsMs:
827 <expand macro="mod_option" value="TMTpro16plex-Lys132N"/> 840 <expand macro="mod_option" value="TMTpro16plex-Lys132N"/>
828 <expand macro="mod_option" value="TMTpro16plex-Lys132C"/> 841 <expand macro="mod_option" value="TMTpro16plex-Lys132C"/>
829 <expand macro="mod_option" value="TMTpro16plex-Lys133N"/> 842 <expand macro="mod_option" value="TMTpro16plex-Lys133N"/>
830 <expand macro="mod_option" value="TMTpro16plex-Lys133C"/> 843 <expand macro="mod_option" value="TMTpro16plex-Lys133C"/>
831 <expand macro="mod_option" value="TMTpro16plex-Lys134N"/> 844 <expand macro="mod_option" value="TMTpro16plex-Lys134N"/>
845 <expand macro="mod_option" value="TMTpro18plex-Nter134C"/>
846 <expand macro="mod_option" value="TMTpro18plex-Nter135N"/>
847 <expand macro="mod_option" value="TMTpro18plex-Lys134C"/>
848 <expand macro="mod_option" value="TMTpro18plex-Lys135N"/>
832 </xml> 849 </xml>
833 <xml name="citations"> 850 <xml name="citations">
834 <citations> 851 <citations>
835 <citation type="bibtex"> 852 <citation type="bibtex">
836 @article{cox2008maxquant, 853 @article{cox2008maxquant,