Mercurial > repos > galaxyp > mqppep_anova
annotate mqppep_anova.xml @ 1:08678c931f5d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
author | galaxyp |
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date | Fri, 28 Oct 2022 18:27:21 +0000 |
parents | dbff53e6f75f |
children | dda27b9273a8 |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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1 <tool |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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2 id="mqppep_anova" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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3 name="MaxQuant Phosphopeptide ANOVA" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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5 profile="21.05" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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6 > |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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7 <description>Runs ANOVA and KSEA for phosphopeptides.</description> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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8 <macros> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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9 <import>macros.xml</import> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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10 <xml name="group_matching_parm"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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11 <param name="group_filter_mode" type="select" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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12 help="Regular expression matching mode 'fixed', 'perl', or 'grep' with option for case insensitivity. See https://rdrr.io/r/base/grep.html" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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13 label="Sample-group matching mode" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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14 > |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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15 <option value="r">ERE ("extended regular expressions")</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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16 <option value="ri"> - ERE, case insensitive</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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17 <option value="p" selected="true">PCRE ("PERL-compatible regular expressions")</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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18 <option value="pi"> - PCRE, case insensitive</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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19 <option value="f">fixed strings ("no regular expressions")</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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20 <option value="fi"> - fixed strings, case insensitive</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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21 </param> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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22 <param name="group_filter_patterns" type="text" value=".+" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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23 help="Comma-separated list of regular expressions matching group-names" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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24 label="Sample-group matching pattern"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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25 <sanitizer> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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26 <valid initial="string.printable"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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27 <remove value="'"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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28 </valid> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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29 </sanitizer> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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30 </param> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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31 </xml> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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32 </macros> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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33 <edam_topics> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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34 <edam_topic>topic_0121</edam_topic><!-- proteomics --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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35 <edam_topic>topic_3520</edam_topic><!-- proteomics experiment--> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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36 </edam_topics> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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37 <edam_operations> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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38 <edam_operation>operation_0276</edam_operation><!-- Analyse a network of protein interactions. --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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39 <edam_operation>operation_0531</edam_operation><!-- Heat map generation --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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40 <edam_operation>operation_2938</edam_operation><!-- Dendrogram generation --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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41 <edam_operation>operation_2938</edam_operation><!-- Imputation --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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42 <edam_operation>operation_3435</edam_operation><!-- Standardisation and normalisation --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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43 <edam_operation>operation_3501</edam_operation><!-- Enrichment analysis --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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44 <edam_operation>operation_3658</edam_operation><!-- Statistical inference --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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45 </edam_operations> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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46 <expand macro="requirements"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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47 <!-- |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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48 The weird invocation used here is because knitr and install_tinytex |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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49 both need access to a writeable directory, but most directories in a |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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50 biocontainer are read-only, so this builds a pseudo-home under /tmp |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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51 --> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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52 <required_files> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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53 <include path="KSEA_impl_flowchart.pdf" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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54 <include path="kinase_name_uniprot_lut.tabular.bz2" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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55 <include path="kinase_uniprot_description_lut.tabular.bz2" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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56 <include path="kinase_uniprot_description_lut.tabular.bz2" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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57 <include path="mqppep_anova.R" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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58 <include path="mqppep_anova_preamble.tex" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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59 <include path="mqppep_anova_script.Rmd" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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60 <include path="perpage.tex" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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61 </required_files> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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62 <command detect_errors="exit_code"><![CDATA[ |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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63 (printenv | sort) && |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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64 cp '$__tool_directory__/mqppep_anova_script.Rmd' . && |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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65 cp '$__tool_directory__/mqppep_anova.R' . && |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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66 cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . && |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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67 cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . && |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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68 cp '$__tool_directory__/mqppep_anova_preamble.tex' . && |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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69 cp '$__tool_directory__/perpage.tex' . && |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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70 cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . && |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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71 Rscript mqppep_anova.R |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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72 --inputFile '$input_file' |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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73 --alphaFile '$alpha_file' |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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74 --preproc_sqlite '$preproc_sqlite' |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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75 --firstDataColumn '$intensity_column_regex_f' |
0
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76 --imputationMethod $imputation.imputation_method |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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77 #if $imputation.imputation_method == "random" |
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78 --meanPercentile '$imputation.meanPercentile' |
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79 --sdPercentile '$imputation.sdPercentile' |
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80 #end if |
1
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81 --regexSampleNames '$sample_names_regex_f' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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82 --regexSampleGrouping '$sample_grouping_regex_f' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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83 #if $group_filter.group_filter_method == "none" |
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84 --sampleGroupFilter 'none' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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85 #else |
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86 --sampleGroupFilter '$group_filter.group_filter_method' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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87 --sampleGroupFilterPatterns '$group_filter_patterns_f' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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88 --sampleGroupFilterMode '$group_filter.group_filter_mode' |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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89 #end if |
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90 --intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp' |
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91 --imputedDataFile '$imputed_data_file' |
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92 --imputedQNLTDataFile '$imp_qn_lt_file' |
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93 --ksea_sqlite '$ksea_sqlite' |
1
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94 --kseaMinSubstrateCount '$ksea_min_substrate_count' |
0
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95 --ksea_cutoff_threshold '$ksea_cutoff_threshold' |
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96 --ksea_cutoff_statistic 'FDR' |
1
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97 --kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc' |
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98 --minQuality '$ksea_min_quality' |
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99 --anova_ksea_metadata '$anova_ksea_metadata' |
1
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100 --reportFile '$report_file' |
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101 ]]></command> |
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102 <!-- |
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103 --> |
0
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104 <configfiles> |
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105 <configfile name="sample_names_regex_f"> |
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106 $sample_names_regex |
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107 </configfile> |
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108 <configfile name="sample_grouping_regex_f"> |
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109 $sample_grouping_regex |
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110 </configfile> |
1
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111 <configfile name="group_filter_patterns_f"> |
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112 #if $group_filter.group_filter_method != "none" |
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113 $group_filter.group_filter_patterns |
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114 #end if |
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115 </configfile> |
0
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116 <configfile name="intensity_column_regex_f"> |
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117 $intensity_column_regex |
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118 </configfile> |
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119 </configfiles> |
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120 <inputs> |
1
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121 <!-- |
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122 needed inputs: |
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123 - # should filters be used to identify sample-groups to be included or excluded |
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124 sampleGroupFilter: !r c("none", "exclude", "include")[3] |
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125 - # what patterns should be used to match sample-groups |
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126 # (extracted by regexSampleGrouping) when determining sample-groups |
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127 # that should be included or excluded |
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128 sampleGroupFilterPatterns: ".*CR,N.*" |
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129 - # minimum number of observed values per class |
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130 intensityMinPerClass: 0 |
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131 - # what should be the primary criterion to eliminate excessive heatmap rows |
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132 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1] |
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133 suggested or advanced inputs: |
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134 - kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2" |
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135 - kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" |
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136 --> |
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137 <param name="input_file" type="data" format="tabular" label="Filtered phosphopeptide intensities (tabular)" |
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138 help="'preproc_tab' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool" |
0
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139 /> |
1
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140 <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level (tabular)" |
0
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141 help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header" |
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142 /> |
1
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143 <param name="preproc_sqlite" type="data" format="sqlite" label="Database from mqppep_preproc (sqlite)" |
0
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144 help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool" |
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145 /> |
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146 <param name="intensity_column_regex" type="text" value="^Intensity[^_]" |
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147 label="Intensity-column pattern" |
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148 help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)" |
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149 /> |
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150 <!-- imputation_method <- c("group-median","median","mean","random")[1] --> |
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151 <conditional name="imputation"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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152 <param name="imputation_method" type="select" label="Imputation method" |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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153 help="Impute missing values by (1) using median for each sample-group; (2) using median across all samples; (3) using mean across all samples; or (4) using randomly generated values having same SD as across all samples (with mean specified by 'Mean percentile for random values')" |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
154 > |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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155 <option value="random" selected="true">random</option> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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156 <option value="group-median">group-median</option> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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157 <option value="median">median</option> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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158 <option value="mean">mean</option> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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159 </param> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
160 <when value="group-median" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
161 <when value="median" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
162 <when value="mean" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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163 <when value="random"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
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164 <param name="meanPercentile" type="integer" value="1" min="1" max="99" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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165 label="Mean percentile for random values" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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166 help="Percentile center of random values; range [1,99]" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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changeset
|
167 /> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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168 <param name="sdPercentile" type="float" value="1" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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169 label="Percentile SD for random values" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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170 help="Standard deviation adjustment-factor for random values; real number. (1.0 means SD of random values equal to the SD for the entire data set.)" |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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171 /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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172 </when> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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173 </conditional> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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174 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$" |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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175 help="Pattern extracting sample-names from names of columns of 'Filtered phosphopeptide intensities' that have peptide intensity data (PERL-compatible regular expression)" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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changeset
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176 label="Sample-name extraction pattern"> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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177 <sanitizer> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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178 <valid initial="string.printable"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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179 <remove value="'"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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180 </valid> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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181 </sanitizer> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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182 </param> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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183 <param name="sample_grouping_regex" type="text" value="\d+" |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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184 help="Pattern extracting sample-group from the extracted sample-names (PERL-compatible regular expression)" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
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185 label="Sample-group extraction pattern"> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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186 <sanitizer> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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187 <valid initial="string.printable"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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188 <remove value="'"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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189 </valid> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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190 </sanitizer> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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191 </param> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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0
diff
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192 <param name="intnsty_min_vals_per_smpl_grp" type="integer" value="1" min="0" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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193 label="Minimum number of values per sample-group" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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194 help="Only consider as comparable those intensities having at least this number of values in each sample-group (range [0,∞])" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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|
195 /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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196 <conditional name="group_filter"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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197 <param name="group_filter_method" type="select" label="Filter sample-groups" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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198 help="What filter should be applied to sample-group names? (1) 'none', no filter; (2) 'include', match is required; (3) 'exclude', match is forbidden." |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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199 > |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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200 <option value="none" selected="true">none</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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201 <option value="include">include</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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202 <option value="exclude">exclude</option> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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203 </param> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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204 <when value="none" /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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205 <when value="include"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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206 <expand macro="group_matching_parm"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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207 </when> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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208 <when value="exclude"> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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209 <expand macro="group_matching_parm"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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210 </when> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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211 </conditional> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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212 <param name="ksea_min_substrate_count" type="integer" value="1" min="1" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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213 label="Minimum number of kinase-substrates for KSEA" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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214 help="Minimum number of substrates to consider any kinase for KSEA (range [1,∞])" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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215 /> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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216 <param name="ksea_cutoff_threshold" type="float" value="0.05" |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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217 label="KSEA threshold level" |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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218 help="Maximum FDR to be used to score a kinase enrichment as significant; see warning against setting this too low in help text below." |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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219 /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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220 <param name="ksea_use_absolute_log2_fc" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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221 type="boolean" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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222 label="Use abs(log2(fold-change)) for KSEA" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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223 help="Should log2(fold-change) be used for KSEA? (Checking this may alter (possibly reduce) the number of hits.)" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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224 checked="false" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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225 truevalue="TRUE" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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226 falsevalue="FALSE" |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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|
227 /> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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228 <param name="ksea_min_quality" type="integer" value="0" min="0" |
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229 label="Minimum quality of substrates for KSEA" |
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230 help="Minimum 'quality' of substrates to be considered for KSEA (range [0,∞]); higher numbers reduce the number of substrates considered - see help text below." |
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231 /> |
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232 </inputs> |
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233 <outputs> |
1
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234 <!-- earlier outputs will appear lower in the history list; therefore, put report at the top --> |
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235 <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite" /> |
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236 <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" /> |
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237 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" /> |
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238 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" /> |
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239 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" /> |
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240 </outputs> |
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241 <tests> |
1
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242 <test><!-- test #1 --> |
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243 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> |
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244 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> |
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245 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> |
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246 <param name="intensity_column_regex" value="^Intensity[^_]"/> |
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247 <param name="imputation_method" value="median"/> |
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248 <param name="sample_names_regex" value="\.\d+[A-Z]$"/> |
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249 <param name="sample_grouping_regex" value="\d+"/> |
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250 <output name="imputed_data_file"> |
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251 <assert_contents> |
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252 <has_text text="Phosphopeptide" /> |
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253 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
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254 <!-- missing missing observd missing observd observd --> |
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255 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" /> |
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256 |
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257 </assert_contents> |
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258 </output> |
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259 <output name="imp_qn_lt_file"> |
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260 <assert_contents> |
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261 <has_text text="Phosphopeptide" /> |
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262 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
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263 <!-- missing missing observed missing observed observed --> |
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264 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.962256.*6.908828.*6.814580.*6.865411.*6.908828.*7.093748" /> |
0
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265 |
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266 <has_text text="pSQKQEEENPAEETGEEK" /> |
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267 </assert_contents> |
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268 </output> |
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269 </test> |
1
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270 <test><!-- test #2 --> |
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271 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> |
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272 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> |
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273 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> |
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274 <param name="intensity_column_regex" value="^Intensity[^_]"/> |
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275 <param name="imputation_method" value="mean"/> |
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276 <!-- |
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277 <param name="meanPercentile" value="1"/> |
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278 <param name="sdPercentile" value="1"/> |
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279 --> |
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280 <param name="sample_names_regex" value="\.\d+[A-Z]$"/> |
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281 <param name="sample_grouping_regex" value="\d+"/> |
1
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282 <param name="intnsty_min_vals_per_smpl_grp" value="1"/> |
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283 <param name="group_filter_method" value="none"/> |
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284 <!-- |
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285 <param name="group_filter_mode" value="r"/> |
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286 <param name="group_filter_patterns" value="\.+"/> |
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287 --> |
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288 <param name="ksea_min_substrate_count" value="1"/> |
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289 <param name="ksea_cutoff_threshold" value="0.5"/> |
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290 <output name="imputed_data_file"> |
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291 <assert_contents> |
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292 <has_text text="Phosphopeptide" /> |
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293 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
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294 <!-- missing missing observd missing observd observd --> |
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295 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" /> |
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296 |
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297 </assert_contents> |
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298 </output> |
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299 <output name="imp_qn_lt_file"> |
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300 <assert_contents> |
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301 <has_text text="Phosphopeptide" /> |
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|
302 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
303 <!-- missing missing observed missing observed observed --> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
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304 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.839850.*6.797424.*6.797424.*6.797424.*6.896609.*7.097251" /> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
305 </assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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306 </output> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
307 </test> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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308 <test><!-- test #3 --> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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309 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
310 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
311 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
312 <param name="intensity_column_regex" value="^Intensity[^_]"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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313 <param name="imputation_method" value="group-median"/> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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314 <!-- |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
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|
315 <param name="meanPercentile" value="1"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
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|
316 <param name="sdPercentile" value="1"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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|
317 --> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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318 <param name="sample_names_regex" value="\.\d+[A-Z]$"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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319 <param name="sample_grouping_regex" value="\d+"/> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
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|
320 <param name="intnsty_min_vals_per_smpl_grp" value="1"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
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|
321 <param name="group_filter_method" value="none"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
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|
322 <!-- |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
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|
323 <param name="group_filter_mode" value="r"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
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|
324 <param name="group_filter_patterns" value="\.+"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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|
325 --> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
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|
326 <param name="ksea_min_substrate_count" value="1"/> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
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|
327 <param name="ksea_cutoff_threshold" value="0.5"/> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
328 <output name="imputed_data_file"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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329 <assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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330 <has_text text="Phosphopeptide" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
331 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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|
332 <!-- missing missing observd missing observd observd --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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333 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
334 |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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335 </assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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336 </output> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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337 <output name="imp_qn_lt_file"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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338 <assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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339 <has_text text="Phosphopeptide" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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|
340 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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341 <!-- missing missing observed missing observed observed --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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342 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.946112.*6.888985.*6.792137.*6.792137.*6.888985.*7.089555" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
343 </assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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344 </output> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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345 </test> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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346 <test><!-- test #4 --> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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347 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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|
348 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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349 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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350 <param name="intensity_column_regex" value="^Intensity[^_]"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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351 <param name="imputation_method" value="random"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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352 <param name="meanPercentile" value="1" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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353 <param name="sdPercentile" value="1.0" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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354 <param name="sample_names_regex" value="\.\d+[A-Z]$"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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355 <param name="sample_grouping_regex" value="\d+"/> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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356 <output name="imputed_data_file"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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357 <assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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358 <has_text text="Phosphopeptide" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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359 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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360 <!-- observd observd observd --> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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361 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.*2355900.*4706000" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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362 |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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363 </assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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364 </output> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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365 <output name="imp_qn_lt_file"> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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366 <assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
367 <has_text text="Phosphopeptide" /> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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368 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" /> |
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
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|
369 <has_text text="5.522821" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B --> |
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
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|
370 <has_text text="6.638251" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A --> |
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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371 </assert_contents> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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372 </output> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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373 </test> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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374 </tests> |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
375 <help><![CDATA[ |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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|
376 ==================================================== |
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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377 Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA |
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378 ==================================================== |
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379 |
1
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380 **Overview** |
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381 ============ |
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382 |
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383 Perform statistical analysis of preprocessed MaxQuant output data collected as described in `[Cheng, 2018] <https://doi.org/10.3791/57996>`_. |
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384 |
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385 - Extracts sample-group IDs from sample names. |
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386 - Imputes missing values. |
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387 - Performs ANOVA analysis for each phosphopeptide. |
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388 - Performs Kinase-Substrate Enrichment Analysis (KSEA) using the method described by `Casado et al. (2013) <doi:10.1126/scisignal.2003573>`_; see *"Algorithms"* section below. |
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389 |
1
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390 **Workflow position** |
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391 ===================== |
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392 |
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393 Upstream tool |
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394 The "MaxQuant Phosphopeptide Preprocessing" tool (``mqppep_preproc``) that transforms MaxQuant output for phospoproteome-enriched samples into a form suitable for statistical analysis. |
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395 |
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396 **Input datasets** |
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397 ================== |
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398 |
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399 ``Filtered phosphopeptide intensities`` (tabular) |
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400 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format). |
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401 This is the output from the "MaxQuant Phopsphopeptide Preprocessing" |
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402 (``mqppep_preproc``) tool. |
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403 |
1
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404 - First column label 'Phosphopeptide'. |
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405 - Sample-intensities must begin in first column matching 'Intensity-column pattern' and must have column labels to match argument 'Sample-name extraction pattern'. |
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406 |
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407 ``ANOVA alpha cutoff level`` (tabular) |
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408 List of alpha cutoff values for significance testing; text file having one column and no header. For example: |
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409 |
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410 :: |
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411 |
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412 0.2 |
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413 0.1 |
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414 0.05 |
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415 |
1
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416 ``Database from mqppep_preproc`` (sqlite) |
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417 SQLite database produced by the "MaxQuant Phopsphopeptide Preprocessing" |
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418 (``mqppep_preproc``) tool. |
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419 |
0
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420 **Input parameters** |
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421 ==================== |
0
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422 |
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423 ``Intensity-column pattern`` |
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424 First column of ``Filtered phosphopeptide intensities`` having intensity values (integer or PERL-compatible regular expression matching column label). Default:: |
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425 |
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426 ^Intensity[^_] |
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427 |
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428 ``Imputation method`` |
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429 Impute missing values by: |
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430 |
1
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431 1. ``group-median`` - use median for each sample-group; |
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432 2. ``mean`` - use mean across all samples; or |
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433 3. ``median`` - use median across all samples; |
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434 4. ``random`` - use randomly generated values where: |
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435 |
1
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436 (i) ``Mean percentile for random values`` specifies the percentile among non-missing values to be used as mean of random values, and |
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437 (ii) ``Percentile SD for random values`` specifies the factor to be multiplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values. |
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438 |
1
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439 ``Sample-name extraction pattern`` |
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440 PERL-compatible regular expression extracting the sample-name from the the name of a column of intensities (from ``Filtered phosphopeptide intensities``) for one sample. |
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441 |
1
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442 - For example, ``"\.\d+[A-Z]$"`` applied to "``Intensity.splunge.10A``" would produce "``.10A``". |
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443 - Note that *this is case sensitive* by default. |
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444 |
1
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445 ``Sample-group extraction pattern`` |
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446 PERL-compatible regular expression extracting the sample-grouping from the sample-name (that was in turn extracted with ``Sample-name extraction pattern`` from a column of intensites from ``Filtered phosphopeptide intensities``). |
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447 |
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448 - For example, ``"\d+$"`` applied to "``.10A``" would produce "``10``". |
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449 - Note that *this is case sensitive* by default. |
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450 |
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451 ``Minimum number of values per sample-group`` |
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452 Sometimes you may wish to filter out the intensities that are poorly represented among some sample groups because they complicate the comparison process. You can use this parameter to specify the minimum number of values in any sample-group (range [0,]]>∞<![CDATA[]) |
0
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453 |
1
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454 ``Filter sample-groups`` |
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455 Sometimes you may have spectra that are for treatments that you are not considering for your comparison. You can specify a filter (or not) for sample-group names; if you do, you can specify whether groups that match your criteria should be excluded from the analysis ("forbidden") or included in the analysis ("required"). |
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456 |
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457 ``Sample-group matching mode`` |
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458 The R `base::grep` function that is used here for pattern matching is exhaustively documented at https://rdrr.io/r/base/grep.html. There are two choices you make here. The first is whether to differentiate lowercase and uppercase characters. The second is wheter to require exact matches ("fixed" pattern-matching mode) or to use "PERL-compatible regular expressions) ("perl") or "extendd regular expressions" ("grep"). See https://rdrr.io/r/base/grep.html for further info. |
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459 |
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460 ``Sample-group matching pattern`` |
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461 This is a comma-separated list of patterns to match to group-names, according to the ``Sample-group matching mode`` that you have chosen. |
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462 |
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463 ``Minimum number of kinase-substrates for KSEA`` |
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464 For KSEA, you may decide that you wish to ignore kinases having fewer substrates than some minimum; specify that minimum here (range [1,]]>∞<![CDATA[]) |
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465 |
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466 ``KSEA threshold level`` |
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467 Specifies minimum FDR at which a kinase will be considered to be enriched; the default choice of ``0.05`` is arbitrary and may exclude kinases that are interesting. The KSEA FDR perhaps should not be treated as conservatively as would be appropriate for hypothesis testing. For example, at an FDR of ``0.05``, for every ``20`` kinases that on discards, ``19`` are likely truely enriched. |
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468 |
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469 ``Use abs(log2(fold-change)) for KSEA`` |
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470 When TRUE, consider only the magnitude of the differences across the contrast for all of the substrates when aggregating them to assess the enrichment of a given kinase's substrates. When FALSE, also consider the direction. Surprisingly, setting this to TRUE may decrease the enriched kinases. |
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471 |
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472 ``Minimum quality of substrates for KSEA`` |
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473 An arbitrary "quality score" is assigned to each substrate, as described in the PDF report produced by the tool. This score takes into account both FDR-adjusted p-value and the number of missing values for each substrate. Setting the minimum to zero retains all substrates, which may be a large number. |
0
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474 |
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475 **Outputs** |
1
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476 =========== |
0
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477 |
1
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478 Report dataset |
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479 *[input file].[imputation method]*-``imputed_report`` |
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480 |
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481 Summary report for normalization, imputation, and **ANOVA**, in PDF format. |
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482 |
1
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483 Imputed intensities |
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484 *[input file].[imputation method]*-``imputed_intensities`` |
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485 |
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486 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, in tabular format. |
0
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487 |
1
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488 Imputed quantum-normalized log-transformed intensities |
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489 *[input file].[imputation method]*-``imputed_QN_LT_intensities`` |
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490 |
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491 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format. |
0
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492 |
1
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493 ANOVA KSEA metadata |
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494 *[input file].[imputation method]*-``imputed_anova_ksea_metadata`` |
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495 Phosphopeptide metadata including ANOVA significance and KSEA enrichments. |
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496 |
1
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497 KSEA SQLite database sqlite |
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498 *[input file].[imputation method]*-``imputed_ksea_sqlite`` |
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499 An SQLite database that is usable for *ad hoc* report creation. |
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500 |
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501 **Algorithm** |
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502 ============= |
0
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503 |
1
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504 The KSEA algorithm used here is as in the KSEAapp package as reported in `[Wiredja 2017] <https://doi.org/10.1093/bioinformatics/btx415>`_. |
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505 The code is adapted from `"Danica D. Wiredja (2017). KSEAapp: Kinase-Substrate Enrichment Analysis. R package version 0.99.0." <https://cran.r-project.org/package=KSEAapp>`_ to work with output from the "MaxQuant Phosphopeptide Preprocessing" Galaxy tool and the multiple kinase-substrate databases that the latter tool searches. |
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506 |
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507 **Authors** |
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508 =========== |
0
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509 |
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510 ``Larry C. Cheng`` |
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511 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script. |
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512 |
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513 ``Arthur C. Eschenlauer`` |
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514 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. |
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515 |
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516 =================================== |
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517 PERL-compatible regular expressions |
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518 =================================== |
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519 |
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520 Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html |
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521 |
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522 ]]></help> |
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523 <citations> |
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524 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 --> |
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525 <citation type="doi">10.3791/57996</citation> |
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526 <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 --> |
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527 <citation type="doi">10.1093/bioinformatics/btx415</citation> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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528 <citation type="bibtex">@Manual{, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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529 title = {KSEAapp: Kinase-Substrate Enrichment Analysis}, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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530 author = {Danica D. Wiredja}, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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531 year = {2017}, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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532 note = {R package version 0.99.0}, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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533 }</citation> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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534 </citations> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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535 </tool> |