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comparison macros.xml @ 11:d72c96ad9a16 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
author galaxyp
date Tue, 15 Jun 2021 07:55:59 +0000
parents f522c08e900c
children 0839f84def5e
comparison
equal deleted inserted replaced
10:f522c08e900c 11:d72c96ad9a16
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">1.6.10.43</token> 3 <token name="@VERSION@">1.6.10.43</token>
4 <token name="@VERSION_PTXQC@">1.0.9</token>
4 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> 5 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
5 <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True] 6 <token name="@TMT2PLEX@">
7 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
8 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
9 </token>
10 <token name="@TMT6PLEX@">
11 - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
12 - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
13 - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
14 - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
15 - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
16 - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
17 </token>
18 <token name="@TMT8PLEX@">
19 - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
20 - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
21 - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
22 - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
23 - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
24 - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
25 - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
26 - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
27 </token>
28 <token name="@TMT10PLEX@">
29 - [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
6 - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True] 30 - [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
7 - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True] 31 - [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
8 - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True] 32 - [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
9 - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True] 33 - [TMT10plex-Lys128C,TMT10plex-Nter128C,0,0,0,0,True]
10 - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True] 34 - [TMT10plex-Lys129N,TMT10plex-Nter129N,0,0,0,0,True]
11 - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True] 35 - [TMT10plex-Lys129C,TMT10plex-Nter129C,0,0,0,0,True]
12 - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True] 36 - [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
13 - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True] 37 - [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
14 - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True] 38 - [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
15 ]]></token> 39 </token>
16 40 <token name="@TMT11PLEX@">
41 @TMT10PLEX@
42 - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
43 </token>
44 <token name="@ITRAQ4PLEX@">
45 - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
46 - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
47 - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
48 - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
49 </token>
50 <token name="@ITRAQ8PLEX@">
51 - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
52 @ITRAQ4PLEX@
53 - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
54 - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
55 - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
56 </token>
57 <token name="@IODOTMT6PLEX@">
58 - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
59 - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
60 - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
61 - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
62 - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
63 - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
64 </token>
17 <xml name="requirements"> 65 <xml name="requirements">
18 <requirements> 66 <requirements>
19 <requirement type="package" version="@VERSION@">maxquant</requirement> 67 <requirement type="package" version="@VERSION@">maxquant</requirement>
20 <requirement type="package" version="3.7">python</requirement> 68 <requirement type="package" version="3.7">python</requirement>
21 <requirement type="package" version="5.1.2">pyyaml</requirement> 69 <requirement type="package" version="5.1.2">pyyaml</requirement>
22 <requirement type="package" version="0.92.6">r-ptxqc</requirement> 70 <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>
23 <requirement type="package" version="1.32">tar</requirement> 71 <requirement type="package" version="1.32">tar</requirement>
24 </requirements> 72 </requirements>
25 </xml> 73 </xml>
26
27 <xml name="ptxqc"> 74 <xml name="ptxqc">
28 <configfile name="qr_yaml"> 75 <configfile name="qr_yaml">
29 PTXQC: 76 PTXQC:
30 ReportFilename: 77 ReportFilename:
31 extended: yes 78 extended: yes
117 qcMetric_EVD_ProteinCount: 450.0 164 qcMetric_EVD_ProteinCount: 450.0
118 qcMetric_AverageQualOverall: 9999.0 165 qcMetric_AverageQualOverall: 9999.0
119 </configfile> 166 </configfile>
120 <configfile name="qr"> 167 <configfile name="qr">
121 library(PTXQC) 168 library(PTXQC)
169 library(data.table)
122 library(yaml) 170 library(yaml)
123 library(methods) 171 library(methods)
124 args = commandArgs(trailingOnly=TRUE) 172 args = commandArgs(trailingOnly=TRUE)
125 yaml_config = yaml.load_file(input = args[1]) 173 yaml_config = yaml.load_file(input = args[1])
126 r = createReport('./combined/txt', yaml_config) 174 r = createReport('./combined/txt', yaml_obj=yaml_config)
127 cat(paste0("\nReport generated as '", r\$report_file, "'\n\n")) 175 cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
128 </configfile> 176 </configfile>
129 </xml> 177 </xml>
130
131 <xml name="mod_option" token_value="default"> 178 <xml name="mod_option" token_value="default">
132 <option value="@VALUE@">@VALUE@</option> 179 <option value="@VALUE@">@VALUE@</option>
133 </xml> 180 </xml>
134 <xml name="default_mod_option" token_value="default"> 181 <xml name="default_mod_option" token_value="default">
135 <option selected="true" value="@VALUE@">@VALUE@</option> 182 <option selected="true" value="@VALUE@">@VALUE@</option>
136 </xml> 183 </xml>
137
138 <xml name="ptxqc-opts"> 184 <xml name="ptxqc-opts">
139 <conditional name="qc"> 185 <conditional name="qc">
140 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" 186 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/>
141 type="boolean" checked="false"/>
142 <when value="true"> 187 <when value="true">
143 <param name="parameters" type="boolean" checked="true" 188 <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>
144 label="use parameters.txt?" truevalue="yes" falsevalue="no" /> 189 <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>
145 <param name="summary" type="boolean" checked="true" 190 <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/>
146 label="use summary.txt?" truevalue="yes" falsevalue="no" /> 191 <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/>
147 <param name="proteingroups" type="boolean" checked="true" 192 <param name="msms" type="boolean" checked="true" label="use msms.txt?" truevalue="yes" falsevalue="no"/>
148 label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" /> 193 <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/>
149 <param name="evidence" type="boolean" checked="true"
150 label="use evidence.txt?" truevalue="yes" falsevalue="no" />
151 <param name="msms" type="boolean" checked="true"
152 label="use msms.txt?" truevalue="yes" falsevalue="no" />
153 <param name="msmsscans" type="boolean" checked="true"
154 label="use msmsScans.txt?" truevalue="yes" falsevalue="no" />
155 </when> 194 </when>
156 <when value="false"/> 195 <when value="false"/>
157 </conditional> 196 </conditional>
158 </xml> 197 </xml>
159
160 <xml name="outputs"> 198 <xml name="outputs">
161 <outputs> 199 <outputs>
162 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/> 200 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
163 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/> 201 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
164 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/> 202 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
181 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report"> 219 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
182 <filter>qc['do_it'] == True</filter> 220 <filter>qc['do_it'] == True</filter>
183 </data> 221 </data>
184 </outputs> 222 </outputs>
185 </xml> 223 </xml>
186
187 <xml name="modification"> 224 <xml name="modification">
188 <expand macro="mod_option" value="Acetyl (K)"/> 225 <expand macro="mod_option" value="Acetyl (K)"/>
189 <expand macro="mod_option" value="Acetyl (Protein N-term)"/> 226 <expand macro="mod_option" value="Acetyl (Protein N-term)"/>
190 <expand macro="mod_option" value="Carbamidomethyl (C)"/> 227 <expand macro="mod_option" value="Carbamidomethyl (C)"/>
191 <expand macro="mod_option" value="Oxidation (M)"/> 228 <expand macro="mod_option" value="Oxidation (M)"/>
599 <expand macro="mod_option" value="Val-&gt;CamCys"/> 636 <expand macro="mod_option" value="Val-&gt;CamCys"/>
600 <expand macro="mod_option" value="Xle-&gt;CamCys"/> 637 <expand macro="mod_option" value="Xle-&gt;CamCys"/>
601 <expand macro="mod_option" value="Cysteinyl"/> 638 <expand macro="mod_option" value="Cysteinyl"/>
602 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> 639 <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/>
603 </xml> 640 </xml>
604
605 <xml name="label"> 641 <xml name="label">
606 <expand macro="mod_option" value="Arg6"/> 642 <expand macro="mod_option" value="Arg6"/>
607 <expand macro="mod_option" value="Arg10"/> 643 <expand macro="mod_option" value="Arg10"/>
608 <expand macro="mod_option" value="Lys4"/> 644 <expand macro="mod_option" value="Lys4"/>
609 <expand macro="mod_option" value="Lys6"/> 645 <expand macro="mod_option" value="Lys6"/>
636 <expand macro="mod_option" value="DimethLys6"/> 672 <expand macro="mod_option" value="DimethLys6"/>
637 <expand macro="mod_option" value="DimethNter6"/> 673 <expand macro="mod_option" value="DimethNter6"/>
638 <expand macro="mod_option" value="Leu7"/> 674 <expand macro="mod_option" value="Leu7"/>
639 <expand macro="mod_option" value="Ile7"/> 675 <expand macro="mod_option" value="Ile7"/>
640 </xml> 676 </xml>
641
642 <xml name="proteases"> 677 <xml name="proteases">
643 <expand macro="mod_option" value="Trypsin"/> 678 <expand macro="mod_option" value="Trypsin"/>
644 <expand macro="mod_option" value="Trypsin/P"/> 679 <expand macro="mod_option" value="Trypsin/P"/>
645 <expand macro="mod_option" value="LysC"/> 680 <expand macro="mod_option" value="LysC"/>
646 <expand macro="mod_option" value="LysC/P"/> 681 <expand macro="mod_option" value="LysC/P"/>
652 <expand macro="mod_option" value="AspN"/> 687 <expand macro="mod_option" value="AspN"/>
653 <expand macro="mod_option" value="LysN"/> 688 <expand macro="mod_option" value="LysN"/>
654 <expand macro="mod_option" value="Chymotrypsin+"/> 689 <expand macro="mod_option" value="Chymotrypsin+"/>
655 <expand macro="mod_option" value="Chymotrypsin"/> 690 <expand macro="mod_option" value="Chymotrypsin"/>
656 </xml> 691 </xml>
657
658 <xml name="iso_labels"> 692 <xml name="iso_labels">
659 <expand macro="mod_option" value="iTRAQ4plex-Nter114"/> 693 <expand macro="mod_option" value="iTRAQ4plex-Nter114"/>
660 <expand macro="mod_option" value="iTRAQ4plex-Nter115"/> 694 <expand macro="mod_option" value="iTRAQ4plex-Nter115"/>
661 <expand macro="mod_option" value="iTRAQ4plex-Nter116"/> 695 <expand macro="mod_option" value="iTRAQ4plex-Nter116"/>
662 <expand macro="mod_option" value="iTRAQ4plex-Nter117"/> 696 <expand macro="mod_option" value="iTRAQ4plex-Nter117"/>
739 <expand macro="mod_option" value="iodoTMT6plex-Cys128"/> 773 <expand macro="mod_option" value="iodoTMT6plex-Cys128"/>
740 <expand macro="mod_option" value="iodoTMT6plex-Cys129"/> 774 <expand macro="mod_option" value="iodoTMT6plex-Cys129"/>
741 <expand macro="mod_option" value="iodoTMT6plex-Cys130"/> 775 <expand macro="mod_option" value="iodoTMT6plex-Cys130"/>
742 <expand macro="mod_option" value="iodoTMT6plex-Cys131"/> 776 <expand macro="mod_option" value="iodoTMT6plex-Cys131"/>
743 </xml> 777 </xml>
744 778 <xml name="citations">
745 <xml name="citations">
746 <citations> 779 <citations>
747 <citation type="bibtex"> 780 <citation type="bibtex">
748 @article{cox2008maxquant, 781 @article{cox2008maxquant,
749 title={MaxQuant enables high peptide identification rates, individualized 782 title={MaxQuant enables high peptide identification rates, individualized
750 ppb-range mass accuracies and proteome-wide protein quantification}, 783 ppb-range mass accuracies and proteome-wide protein quantification},