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comparison macros.xml @ 21:8934bc76bb52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb
author galaxyp
date Mon, 19 Jun 2023 17:02:17 +0000
parents 837224ad1694
children 9c52362ae7bb
comparison
equal deleted inserted replaced
20:837224ad1694 21:8934bc76bb52
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="@PROFILE@">21.05</token>
4 <token name="@VERSION_SUFFIX@">7</token> 4 <token name="@VERSION@">2.0.3.0</token>
5 <token name="@VERSION_SUFFIX_MQPAR@">2</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@VERSION_PTXQC@">1.0.10</token> 6 <token name="@VERSION_SUFFIX_MQPAR@">0</token>
7 <token name="@VERSION_PTXQC@">1.0.16</token>
7 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> 8 <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
8 <token name="@TMT2PLEX@"> 9 <token name="@TMT2PLEX@">
9 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] 10 - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
10 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] 11 - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
11 </token> 12 </token>
88 - [iodoTMT6plex-Cys131,'',0,0,0,0,True] 89 - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
89 </token> 90 </token>
90 <xml name="requirements"> 91 <xml name="requirements">
91 <requirements> 92 <requirements>
92 <requirement type="package" version="@VERSION@">maxquant</requirement> 93 <requirement type="package" version="@VERSION@">maxquant</requirement>
93 <requirement type="package" version="3.7">python</requirement> 94 <requirement type="package" version="5.4.1">pyyaml</requirement>
94 <requirement type="package" version="5.1.2">pyyaml</requirement> 95 <requirement type="package" version="3.1.418">dotnet</requirement>
95 <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement> 96 <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement>
96 <requirement type="package" version="1.32">tar</requirement> 97 <requirement type="package" version="1.32">tar</requirement>
97 </requirements> 98 </requirements>
98 </xml> 99 </xml>
99 <xml name="required_files"> 100 <xml name="required_files">
114 - plainPDF 115 - plainPDF
115 PlainPDF: 116 PlainPDF:
116 AddPageNumbers: 'on' 117 AddPageNumbers: 'on'
117 File: 118 File:
118 Parameters: 119 Parameters:
119 #if $qc.do_it: 120 #if $qc.do_it == "true":
120 enabled: ${qc.parameters} 121 enabled: ${qc.parameters}
121 #end if 122 #end if
122 Summary: 123 Summary:
123 #if $qc.do_it: 124 #if $qc.do_it == "true":
124 enabled: ${qc.summary} 125 enabled: ${qc.summary}
125 #end if 126 #end if
126 IDRate: 127 IDRate:
127 Thresh_bad_num: 20.0 128 Thresh_bad_num: 20.0
128 Thresh_great_num: 35.0 129 Thresh_great_num: 35.0
129 ProteinGroups: 130 ProteinGroups:
130 #if $qc.do_it: 131 #if $qc.do_it == "true":
131 enabled: ${qc.proteingroups} 132 enabled: ${qc.proteingroups}
132 #end if 133 #end if
133 RatioPlot: 134 RatioPlot:
134 LabelIncThresh_num: 4.0 135 LabelIncThresh_num: 4.0
135 IntensityThreshLog2_num: 25.0 136 IntensityThreshLog2_num: 25.0
136 Evidence: 137 Evidence:
137 #if $qc.do_it: 138 #if $qc.do_it == "true":
138 enabled: ${qc.evidence} 139 enabled: ${qc.evidence}
139 #end if 140 #end if
140 ProteinCountThresh_num: 3500.0 141 ProteinCountThresh_num: 3500.0
141 IntensityThreshLog2_num: 23.0 142 IntensityThreshLog2_num: 23.0
142 PeptideCountThresh_num: 15000.0 143 PeptideCountThresh_num: 15000.0
159 MatchBetweenRuns_wA: auto 160 MatchBetweenRuns_wA: auto
160 MQpar_firstSearchTol_num: 20.0 161 MQpar_firstSearchTol_num: 20.0
161 firstSearch_outOfCalWarnSD_num: 2.0 162 firstSearch_outOfCalWarnSD_num: 2.0
162 MQpar_mainSearchTol_num: 4.5 163 MQpar_mainSearchTol_num: 4.5
163 MsMs: 164 MsMs:
164 #if $qc.do_it: 165 #if $qc.do_it == "true":
165 enabled: ${qc.msms} 166 enabled: ${qc.msms}
166 #end if 167 #end if
167 MsMsScans: 168 MsMsScans:
168 #if $qc.do_it: 169 #if $qc.do_it == "true":
169 enabled: ${qc.msmsscans} 170 enabled: ${qc.msmsscans}
170 #end if 171 #end if
171 IonInjectionThresh_num: 10.0 172 IonInjectionThresh_num: 10.0
172 order: 173 order:
173 qcMetric_PAR: 1.0 174 qcMetric_PAR: 1.0
220 <xml name="default_mod_option" token_value="default"> 221 <xml name="default_mod_option" token_value="default">
221 <option selected="true" value="@VALUE@">@VALUE@</option> 222 <option selected="true" value="@VALUE@">@VALUE@</option>
222 </xml> 223 </xml>
223 <xml name="ptxqc-opts"> 224 <xml name="ptxqc-opts">
224 <conditional name="qc"> 225 <conditional name="qc">
225 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/> 226 <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="select">
227 <option value="true">True</option>
228 <option value="false" selected="true">False</option>
229 </param>
226 <when value="true"> 230 <when value="true">
227 <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/> 231 <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/>
228 <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/> 232 <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/>
229 <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/> 233 <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/>
230 <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/> 234 <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/>
232 <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/> 236 <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/>
233 </when> 237 </when>
234 <when value="false"/> 238 <when value="false"/>
235 </conditional> 239 </conditional>
236 </xml> 240 </xml>
241
242 <xml name="output" tokens="name,label" token_format="tabular">
243 <data format="@FORMAT@" label="${on_string}: @LABEL@" name="@NAME@">
244 <filter>'@NAME@' in output_opts['output']</filter>
245 </data>
246 </xml>
247 <xml name="output_from_wdir" tokens="name,label" token_ext="txt" token_format="tabular">
248 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="${on_string}: @LABEL@" name="@NAME@">
249 <filter>'@NAME@' in output_opts['output']</filter>
250 </data>
251 </xml>
252
237 <xml name="outputs"> 253 <xml name="outputs">
238 <outputs> 254 <outputs>
239 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/> 255 <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/>
240 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/> 256 <expand macro="output_from_wdir" name="mqpar" label="mqpar.xml" format="xml" ext="xml"/>
241 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/> 257 <expand macro="output_from_wdir" name="peptides" label="MaxQuant Peptides"/>
242 <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/> 258 <expand macro="output_from_wdir" name="evidence" label="MaxQuant Evidence"/>
243 <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/> 259 <expand macro="output_from_wdir" name="parameters" label="MaxQuant Tabular Parameters"/>
244 <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/> 260 <expand macro="output_from_wdir" name="msms" label="MaxQuant MSMS"/>
245 <expand macro="output_from_wdir" name="mzTab" label="mzTab" ext="mzTab"/> 261 <expand macro="output_from_wdir" name="mzTab" label="mzTab" format="mztab" ext="mzTab"/>
246 <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/> 262 <expand macro="output_from_wdir" name="allPeptides" label="all peptides"/>
247 <expand macro="output_from_wdir" name="libraryMatch" label="library match"/> 263 <expand macro="output_from_wdir" name="libraryMatch" label="library match"/>
248 <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/> 264 <expand macro="output_from_wdir" name="matchedFeatures" label="matched features"/>
249 <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/> 265 <expand macro="output_from_wdir" name="modificationSpecificPeptides" label="modification specific peptides"/>
250 <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/> 266 <expand macro="output_from_wdir" name="ms3Scans" label="ms3 scans"/>
254 <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/> 270 <expand macro="output_from_wdir" name="summary" label="MaxQuant summary"/>
255 <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/> 271 <expand macro="output" name="output_all" format="tar" label="'combined/txt/' directory"/>
256 <expand macro="output" name="log" format="txt" label="log"/> 272 <expand macro="output" name="log" format="txt" label="log"/>
257 <expand macro="output" name="config" format="txt" label="yaml config file"/> 273 <expand macro="output" name="config" format="txt" label="yaml config file"/>
258 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report"> 274 <data format="pdf" label="PTXQC report for ${on_string}" name="ptxqc_report">
259 <filter>qc['do_it'] == True</filter> 275 <filter>qc['do_it'] == "true"</filter>
260 </data> 276 </data>
261 </outputs> 277 </outputs>
262 </xml> 278 </xml>
263 <xml name="modification"> 279 <xml name="modification">
264 <expand macro="mod_option" value="Acetyl (K)"/> 280 <expand macro="mod_option" value="Acetyl (K)"/>
851 <expand macro="mod_option" value="TMTpro18plex-Nter134C"/> 867 <expand macro="mod_option" value="TMTpro18plex-Nter134C"/>
852 <expand macro="mod_option" value="TMTpro18plex-Nter135N"/> 868 <expand macro="mod_option" value="TMTpro18plex-Nter135N"/>
853 <expand macro="mod_option" value="TMTpro18plex-Lys134C"/> 869 <expand macro="mod_option" value="TMTpro18plex-Lys134C"/>
854 <expand macro="mod_option" value="TMTpro18plex-Lys135N"/> 870 <expand macro="mod_option" value="TMTpro18plex-Lys135N"/>
855 </xml> 871 </xml>
872
873 <xml name="reporter_ion_macro">
874 <conditional name="iso_labels">
875 <param name="labeling" type="select" label="isobaric labeling"
876 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
877 <option value="custom">custom</option>
878 <option value="tmt2plex">TMT2plex</option>
879 <option value="tmt6plex">TMT6plex</option>
880 <option value="tmt8plex">TMT8plex</option>
881 <option value="tmt10plex">TMT10plex</option>
882 <option value="tmt11plex">TMT11plex</option>
883 <option value="tmtpro16plex">TMTpro16plex</option>
884 <option value="tmtpro18plex">TMTpro18plex</option>
885 <option value="itraq4plex">iTRAQ4plex</option>
886 <option value="itraq8plex">iTRAQ8plex</option>
887 <option value="iodotmt6plex">iodoTMT6plex</option>
888 </param>
889 <when value="tmt2plex"/>
890 <when value="tmt6plex"/>
891 <when value="tmt8plex"/>
892 <when value="tmt10plex"/>
893 <when value="tmt11plex"/>
894 <when value="tmtpro16plex"/>
895 <when value="tmtpro18plex"/>
896 <when value="itraq4plex"/>
897 <when value="itraq8plex"/>
898 <when value="iodotmt6plex"/>
899 <when value="custom">
900 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
901 <param name="internallabel" type="select" label="internal label" help="contains Lys">
902 <expand macro="iso_labels"/>
903 </param>
904 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
905 <option value="">None</option>
906 <expand macro="iso_labels"/>
907 </param>
908 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
909 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
910 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
911 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
912 <param type="boolean" name="tmtlike" checked="false"
913 label="TMT-like"
914 truevalue="True" falsevalue="False"/>
915 </repeat>
916 </when>
917 </conditional>
918 <conditional name="filter_by_pif">
919 <param name="filter_pif" type="select" label="Filter by PIF"
920 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species.">
921 <option value="True">True</option>
922 <option value="False" selected="true">False</option>
923 </param>
924 <when value="True">
925 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
926 max="1"
927 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
928 </when>
929 <when value="False"/>
930 </conditional>
931 </xml>
932
856 <xml name="citations"> 933 <xml name="citations">
857 <citations> 934 <citations>
858 <citation type="bibtex"> 935 <citation type="bibtex">
859 @article{cox2008maxquant, 936 @article{cox2008maxquant,
860 title={MaxQuant enables high peptide identification rates, individualized 937 title={MaxQuant enables high peptide identification rates, individualized