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comparison macros.xml @ 3:009693badefc draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 15:48:19 +0000
parents 4ce8694766e3
children 6fea360ba324
comparison
equal deleted inserted replaced
2:33c911e66d8e 3:009693badefc
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">1.6.3.4</token> 3 <token name="@VERSION@">1.6.10.43</token>
4 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> 4 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
5 <xml name="output" token_format="tabular" token_label="default description" token_name="default"> 5 <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
6 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@"> 6 - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
7 <filter>'@NAME@' in output_opts['output']</filter> 7 - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
8 </data> 8 - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
9 </xml> 9 - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
10 <xml name="output_option" token_label="default label" token_name="default"> 10 - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
11 <option value="@NAME@">@LABEL@</option> 11 - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
12 </xml> 12 - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
13 - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
14 - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
15 ]]></token>
16
17 <xml name="requirements">
18 <requirements>
19 <requirement type="package" version="@VERSION@">maxquant</requirement>
20 <requirement type="package" version="3.7">python</requirement>
21 <requirement type="package" version="5.1.2">pyyaml</requirement>
22 <requirement type="package" version="0.92.6">r-ptxqc</requirement>
23 <requirement type="package" version="1.32">tar</requirement>
24 </requirements>
25 </xml>
26
27 <xml name="ptxqc">
28 <configfile name="qr_yaml">
29 PTXQC:
30 ReportFilename:
31 extended: yes
32 UseLocalMQPar: yes
33 NameLengthMax_num: 10.0
34 OutputFormats:
35 - plainPDF
36 PlainPDF:
37 AddPageNumbers: 'on'
38 File:
39 Parameters:
40 #if $qc.do_it:
41 enabled: ${qc.parameters}
42 #end if
43 Summary:
44 #if $qc.do_it:
45 enabled: ${qc.summary}
46 #end if
47 IDRate:
48 Thresh_bad_num: 20.0
49 Thresh_great_num: 35.0
50 ProteinGroups:
51 #if $qc.do_it:
52 enabled: ${qc.proteingroups}
53 #end if
54 RatioPlot:
55 LabelIncThresh_num: 4.0
56 IntensityThreshLog2_num: 25.0
57 Evidence:
58 #if $qc.do_it:
59 enabled: ${qc.evidence}
60 #end if
61 ProteinCountThresh_num: 3500.0
62 IntensityThreshLog2_num: 23.0
63 PeptideCountThresh_num: 15000.0
64 SpecialContaminants:
65 cont_MYCO:
66 - MYCOPLASMA
67 - '1'
68 MQpar_MatchingTimeWindow_num: 0.0
69 MatchBetweenRuns_wA: auto
70 MQpar_firstSearchTol_num: 20.0
71 firstSearch_outOfCalWarnSD_num: 2.0
72 MQpar_mainSearchTol_num: 4.5
73 MsMs:
74 #if $qc.do_it:
75 enabled: ${qc.msms}
76 #end if
77 MsMsScans:
78 #if $qc.do_it:
79 enabled: ${qc.msmsscans}
80 #end if
81 IonInjectionThresh_num: 10.0
82 order:
83 qcMetric_PAR: 1.0
84 qcMetric_PG_PCA: 3.0
85 qcMetric_EVD_Top5Cont: 10.0
86 qcMetric_PG_Ratio: 19.0
87 qcMetric_EVD_UserContaminant: 20.0
88 qcMetric_EVD_PeptideInt: 30.0
89 qcMetric_EVD_ReporterInt: 31.0
90 qcMetric_PG_RawInt: 32.0
91 qcMetric_PG_LFQInt: 33.0
92 qcMetric_PG_ReporterInt: 34.0
93 qcMetric_MSMS_MissedCleavages: 40.0
94 qcMetric_EVD_Charge: 100.0
95 qcMetric_PG_Cont: 110.0
96 qcMetric_MSMSScans_TopNoverRT: 120.0
97 qcMetric_EVD_IDoverRT: 150.0
98 qcMetric_EVD_RTPeakWidth: 170.0
99 qcMetric_EVD_MBRAlign: 210.0
100 qcMetric_EVD_MBRIdTransfer: 220.0
101 qcMetric_EVD_MBRaux: 221.0
102 qcMetric_MSMSScans_IonInjTime: 240.0
103 qcMetric_MSMSScans_MSMSIntensity: 245.0
104 qcMetric_EVD_MS2OverSampling: 250.0
105 qcMetric_EVD_PreCal: 260.0
106 qcMetric_EVD_PostCal: 270.0
107 qcMetric_MSMS_MSMSDecal: 280.0
108 qcMetric_SM_MSMSIdRate: 300.0
109 qcMetric_MSMSScans_TopNID: 380.0
110 qcMetric_MSMSScans_DepPep: 383.0
111 qcMetric_EVD_MissingValues: 390.0
112 qcMetric_EVD_PeptideCount: 400.0
113 qcMetric_EVD_ProteinCount: 450.0
114 qcMetric_AverageQualOverall: 9999.0
115 </configfile>
116 <configfile name="qr">
117 library(PTXQC)
118 library(yaml)
119 library(methods)
120 args = commandArgs(trailingOnly=TRUE)
121 yaml_config = yaml.load_file(input = args[1])
122 r = createReport('./combined/txt', yaml_config)
123 cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
124 </configfile>
125 </xml>
126
13 <xml name="mod_option" token_value="default"> 127 <xml name="mod_option" token_value="default">
14 <option value="@VALUE@">@VALUE@</option> 128 <option value="@VALUE@">@VALUE@</option>
15 </xml> 129 </xml>
130 <xml name="default_mod_option" token_value="default">
131 <option selected="true" value="@VALUE@">@VALUE@</option>
132 </xml>
133
134 <xml name="ptxqc-opts">
135 <conditional name="qc">
136 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (at own risk)"
137 type="boolean" checked="false"/>
138 <when value="true">
139 <param name="parameters" type="boolean" checked="true"
140 label="use parameters.txt?" truevalue="yes" falsevalue="no" />
141 <param name="summary" type="boolean" checked="true"
142 label="use summary.txt?" truevalue="yes" falsevalue="no" />
143 <param name="proteingroups" type="boolean" checked="true"
144 label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" />
145 <param name="evidence" type="boolean" checked="true"
146 label="use evidence.txt?" truevalue="yes" falsevalue="no" />
147 <param name="msms" type="boolean" checked="true"
148 label="use msms.txt?" truevalue="yes" falsevalue="no" />
149 <param name="msmsscans" type="boolean" checked="true"
150 label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />
151 </when>
152 <when value="false"/>
153 </conditional>
154 </xml>
155
156 <xml name="outputs">
157 <outputs>
158 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
159 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
160 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
161 <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/>
162 <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/>
163 <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/>
164 <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/>
165 <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/>
166 <expand macro="output_from_wdir" name="libraryMatch" label="library match"/>
167 <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/>
168 <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/>
169 <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/>
170 <expand macro="output_from_wdir" name="msmsScans" label="msms Scans"/>
171 <expand macro="output_from_wdir" name="mzRange" label="mz range"/>
172 <expand macro="output_from_wdir" name="peptideSection" label="peptide section"/>
173 <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/>
174 <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/>
175 <expand macro="output" name="log" format="txt" label="log"/>
176 <expand macro="output" name="config" format="txt" label="yaml config file"/>
177 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
178 <filter>qc['do_it'] == True</filter>
179 </data>
180 </outputs>
181 </xml>
182
16 <xml name="modification"> 183 <xml name="modification">
17 <expand macro="mod_option" value="Acetyl (K)"/> 184 <expand macro="mod_option" value="Acetyl (K)"/>
18 <expand macro="mod_option" value="Acetyl (Protein N-term)"/> 185 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
19 <expand macro="mod_option" value="Carbamidomethyl (C)"/> 186 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
20 <expand macro="mod_option" value="Oxidation (M)"/> 187 <expand macro="mod_option" value="Oxidation (M)"/>
428 <expand macro="mod_option" value="Val-&gt;CamCys"/> 595 <expand macro="mod_option" value="Val-&gt;CamCys"/>
429 <expand macro="mod_option" value="Xle-&gt;CamCys"/> 596 <expand macro="mod_option" value="Xle-&gt;CamCys"/>
430 <expand macro="mod_option" value="Cysteinyl"/> 597 <expand macro="mod_option" value="Cysteinyl"/>
431 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> 598 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>
432 </xml> 599 </xml>
600
433 <xml name="label"> 601 <xml name="label">
434 <expand macro="mod_option" value="Arg6"/> 602 <expand macro="mod_option" value="Arg6"/>
435 <expand macro="mod_option" value="Arg10"/> 603 <expand macro="mod_option" value="Arg10"/>
436 <expand macro="mod_option" value="Lys4"/> 604 <expand macro="mod_option" value="Lys4"/>
437 <expand macro="mod_option" value="Lys6"/> 605 <expand macro="mod_option" value="Lys6"/>
464 <expand macro="mod_option" value="DimethLys6"/> 632 <expand macro="mod_option" value="DimethLys6"/>
465 <expand macro="mod_option" value="DimethNter6"/> 633 <expand macro="mod_option" value="DimethNter6"/>
466 <expand macro="mod_option" value="Leu7"/> 634 <expand macro="mod_option" value="Leu7"/>
467 <expand macro="mod_option" value="Ile7"/> 635 <expand macro="mod_option" value="Ile7"/>
468 </xml> 636 </xml>
637
469 <xml name="proteases"> 638 <xml name="proteases">
470 <expand macro="mod_option" value="Trypsin"/> 639 <expand macro="mod_option" value="Trypsin"/>
471 <expand macro="mod_option" value="Trypsin/P"/> 640 <expand macro="mod_option" value="Trypsin/P"/>
472 <expand macro="mod_option" value="LysC"/> 641 <expand macro="mod_option" value="LysC"/>
473 <expand macro="mod_option" value="LysC/P"/> 642 <expand macro="mod_option" value="LysC/P"/>
479 <expand macro="mod_option" value="AspN"/> 648 <expand macro="mod_option" value="AspN"/>
480 <expand macro="mod_option" value="LysN"/> 649 <expand macro="mod_option" value="LysN"/>
481 <expand macro="mod_option" value="Chymotrypsin+"/> 650 <expand macro="mod_option" value="Chymotrypsin+"/>
482 <expand macro="mod_option" value="Chymotrypsin"/> 651 <expand macro="mod_option" value="Chymotrypsin"/>
483 </xml> 652 </xml>
653
654 <xml name="iso_labels">
655 <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>
656 <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>
657 <expand macro="mod_option" value="iTRAQ4plex-Nter116"/>
658 <expand macro="mod_option" value="iTRAQ4plex-Nter117"/>
659 <expand macro="mod_option" value="iTRAQ4plex-Lys114"/>
660 <expand macro="mod_option" value="iTRAQ4plex-Lys115"/>
661 <expand macro="mod_option" value="iTRAQ4plex-Lys116"/>
662 <expand macro="mod_option" value="iTRAQ4plex-Lys117"/>
663 <expand macro="mod_option" value="iTRAQ8plex-Nter113"/>
664 <expand macro="mod_option" value="iTRAQ8plex-Nter114"/>
665 <expand macro="mod_option" value="iTRAQ8plex-Nter115"/>
666 <expand macro="mod_option" value="iTRAQ8plex-Nter116"/>
667 <expand macro="mod_option" value="iTRAQ8plex-Nter117"/>
668 <expand macro="mod_option" value="iTRAQ8plex-Nter118"/>
669 <expand macro="mod_option" value="iTRAQ8plex-Nter119"/>
670 <expand macro="mod_option" value="iTRAQ8plex-Nter121"/>
671 <expand macro="mod_option" value="iTRAQ8plex-Lys113"/>
672 <expand macro="mod_option" value="iTRAQ8plex-Lys114"/>
673 <expand macro="mod_option" value="iTRAQ8plex-Lys115"/>
674 <expand macro="mod_option" value="iTRAQ8plex-Lys116"/>
675 <expand macro="mod_option" value="iTRAQ8plex-Lys117"/>
676 <expand macro="mod_option" value="iTRAQ8plex-Lys118"/>
677 <expand macro="mod_option" value="iTRAQ8plex-Lys119"/>
678 <expand macro="mod_option" value="iTRAQ8plex-Lys121"/>
679 <expand macro="mod_option" value="TMT2plex-Nter126"/>
680 <expand macro="mod_option" value="TMT2plex-Nter127"/>
681 <expand macro="mod_option" value="TMT2plex-Lys126"/>
682 <expand macro="mod_option" value="TMT2plex-Lys127"/>
683 <expand macro="mod_option" value="TMT6plex-Nter126"/>
684 <expand macro="mod_option" value="TMT6plex-Nter127"/>
685 <expand macro="mod_option" value="TMT6plex-Nter128"/>
686 <expand macro="mod_option" value="TMT6plex-Nter129"/>
687 <expand macro="mod_option" value="TMT6plex-Nter130"/>
688 <expand macro="mod_option" value="TMT6plex-Nter131"/>
689 <expand macro="mod_option" value="TMT8plex-Nter126C"/>
690 <expand macro="mod_option" value="TMT8plex-Nter127N"/>
691 <expand macro="mod_option" value="TMT8plex-Nter127C"/>
692 <expand macro="mod_option" value="TMT8plex-Nter128C"/>
693 <expand macro="mod_option" value="TMT8plex-Nter129N"/>
694 <expand macro="mod_option" value="TMT8plex-Nter129C"/>
695 <expand macro="mod_option" value="TMT8plex-Nter130C"/>
696 <expand macro="mod_option" value="TMT8plex-Nter131N"/>
697 <expand macro="mod_option" value="TMT10plex-Nter126C"/>
698 <expand macro="mod_option" value="TMT10plex-Nter127N"/>
699 <expand macro="mod_option" value="TMT10plex-Nter127C"/>
700 <expand macro="mod_option" value="TMT10plex-Nter128N"/>
701 <expand macro="mod_option" value="TMT10plex-Nter128C"/>
702 <expand macro="mod_option" value="TMT10plex-Nter129N"/>
703 <expand macro="mod_option" value="TMT10plex-Nter129C"/>
704 <expand macro="mod_option" value="TMT10plex-Nter130N"/>
705 <expand macro="mod_option" value="TMT10plex-Nter130C"/>
706 <expand macro="mod_option" value="TMT10plex-Nter131N"/>
707 <expand macro="mod_option" value="TMT11plex-Nter131C"/>
708 <expand macro="mod_option" value="TMT6plex-Lys126"/>
709 <expand macro="mod_option" value="TMT6plex-Lys127"/>
710 <expand macro="mod_option" value="TMT6plex-Lys128"/>
711 <expand macro="mod_option" value="TMT6plex-Lys129"/>
712 <expand macro="mod_option" value="TMT6plex-Lys130"/>
713 <expand macro="mod_option" value="TMT6plex-Lys131"/>
714 <expand macro="mod_option" value="TMT8plex-Lys126C"/>
715 <expand macro="mod_option" value="TMT8plex-Lys127N"/>
716 <expand macro="mod_option" value="TMT8plex-Lys127C"/>
717 <expand macro="mod_option" value="TMT8plex-Lys128C"/>
718 <expand macro="mod_option" value="TMT8plex-Lys129N"/>
719 <expand macro="mod_option" value="TMT8plex-Lys129C"/>
720 <expand macro="mod_option" value="TMT8plex-Lys130C"/>
721 <expand macro="mod_option" value="TMT8plex-Lys131N"/>
722 <expand macro="mod_option" value="TMT10plex-Lys126C"/>
723 <expand macro="mod_option" value="TMT10plex-Lys127N"/>
724 <expand macro="mod_option" value="TMT10plex-Lys127C"/>
725 <expand macro="mod_option" value="TMT10plex-Lys128N"/>
726 <expand macro="mod_option" value="TMT10plex-Lys128C"/>
727 <expand macro="mod_option" value="TMT10plex-Lys129N"/>
728 <expand macro="mod_option" value="TMT10plex-Lys129C"/>
729 <expand macro="mod_option" value="TMT10plex-Lys130N"/>
730 <expand macro="mod_option" value="TMT10plex-Lys130C"/>
731 <expand macro="mod_option" value="TMT10plex-Lys131N"/>
732 <expand macro="mod_option" value="TMT11plex-Lys131C"/>
733 <expand macro="mod_option" value="iodoTMT6plex-Cys126"/>
734 <expand macro="mod_option" value="iodoTMT6plex-Cys127"/>
735 <expand macro="mod_option" value="iodoTMT6plex-Cys128"/>
736 <expand macro="mod_option" value="iodoTMT6plex-Cys129"/>
737 <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>
738 <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>
739 </xml>
740
741 <xml name="citations">
742 <citations>
743 <citation type="bibtex">
744 @article{cox2008maxquant,
745 title={MaxQuant enables high peptide identification rates, individualized
746 ppb-range mass accuracies and proteome-wide protein quantification},
747 author={Cox, J{\"u}rgen and Mann, Matthias},
748 journal={Nature biotechnology},
749 volume={26},
750 number={12},
751 pages={1367},
752 year={2008},
753 publisher={Nature Publishing Group}
754 }
755 </citation>
756 <citation type="bibtex">
757 @article{tyanova2016maxquant,
758 title={The MaxQuant computational platform for mass
759 spectrometry-based shotgun proteomics},
760 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
761 journal={Nature protocols},
762 volume={11},
763 number={12},
764 pages={2301},
765 year={2016},
766 publisher={Nature Publishing Group}
767 }
768 </citation>
769 <citation type="doi">10.1021/acs.jproteome.5b00780</citation>
770 </citations>
771 </xml>
484 </macros> 772 </macros>
485