mqppep_anova: mqppep_anova.xml annotate

annotate mqppep_anova.xml @ 5:7d1f8a256cf6 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121

author	galaxyp
date	Fri, 17 Feb 2023 22:38:21 +0000
parents	6f51e262d84d
children

rev	line source
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	1 <tool
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	2 id="mqppep_anova"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	3 name="MaxQuant Phosphopeptide ANOVA"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	5 profile="21.05"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	6 >
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	7 <description>Runs ANOVA and KSEA for phosphopeptides.</description>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	8 <macros>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	9 <import>macros.xml</import>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	10 <xml name="group_matching_parm">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	11 <param name="group_filter_mode" type="select"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	12 help="Regular expression matching mode 'fixed', 'perl', or 'grep' with option for case insensitivity. See https://rdrr.io/r/base/grep.html"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	13 label="Sample-group matching mode"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	14 >
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	15 <option value="r">ERE ("extended regular expressions")</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	16 <option value="ri"> - ERE, case insensitive</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	17 <option value="p" selected="true">PCRE ("PERL-compatible regular expressions")</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	18 <option value="pi"> - PCRE, case insensitive</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	19 <option value="f">fixed strings ("no regular expressions")</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	20 <option value="fi"> - fixed strings, case insensitive</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	21 </param>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	22 <param name="group_filter_patterns" type="text" value=".+"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	23 help="Comma-separated list of regular expressions matching group-names"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	24 label="Sample-group matching pattern">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	25 <sanitizer>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	26 <valid initial="string.printable">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	27 <remove value="'"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	28 </valid>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	29 </sanitizer>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	30 </param>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	31 </xml>
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	32 </macros>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	33 <edam_topics>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	34 <edam_topic>topic_0121</edam_topic><!-- proteomics -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	35 <edam_topic>topic_3520</edam_topic><!-- proteomics experiment-->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	36 </edam_topics>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	37 <edam_operations>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	38 <edam_operation>operation_0276</edam_operation><!-- Analyse a network of protein interactions. -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	39 <edam_operation>operation_0531</edam_operation><!-- Heat map generation -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	40 <edam_operation>operation_2938</edam_operation><!-- Dendrogram generation -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	41 <edam_operation>operation_2938</edam_operation><!-- Imputation -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	42 <edam_operation>operation_3435</edam_operation><!-- Standardisation and normalisation -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	43 <edam_operation>operation_3501</edam_operation><!-- Enrichment analysis -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	44 <edam_operation>operation_3658</edam_operation><!-- Statistical inference -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	45 </edam_operations>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	46 <expand macro="requirements"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	47 <!--
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	48 The weird invocation used here is because knitr and install_tinytex
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	49 both need access to a writeable directory, but most directories in a
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	50 biocontainer are read-only, so this builds a pseudo-home under /tmp
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	51 -->
3 6f51e262d84d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869 galaxyp parents: 1 diff changeset	52 <!-- commenting out to appease linter
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	53 <required_files>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	54 <include path="KSEA_impl_flowchart.pdf" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	55 <include path="kinase_name_uniprot_lut.tabular.bz2" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	56 <include path="kinase_uniprot_description_lut.tabular.bz2" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	57 <include path="kinase_uniprot_description_lut.tabular.bz2" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	58 <include path="mqppep_anova.R" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	59 <include path="mqppep_anova_preamble.tex" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	60 <include path="mqppep_anova_script.Rmd" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	61 <include path="perpage.tex" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	62 </required_files>
3 6f51e262d84d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869 galaxyp parents: 1 diff changeset	63 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	64 <command detect_errors="exit_code"><![CDATA[
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	65 (printenv \| sort) &&
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	66 cp '$__tool_directory__/mqppep_anova_script.Rmd' . &&
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	67 cp '$__tool_directory__/mqppep_anova.R' . &&
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	68 cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . &&
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	69 cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . &&
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	70 cp '$__tool_directory__/mqppep_anova_preamble.tex' . &&
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	71 cp '$__tool_directory__/perpage.tex' . &&
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	72 cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . &&
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	73 Rscript mqppep_anova.R
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	74 --inputFile '$input_file'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	75 --alphaFile '$alpha_file'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	76 --preproc_sqlite '$preproc_sqlite'
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	77 --firstDataColumn '$intensity_column_regex_f'
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	78 --imputationMethod $imputation.imputation_method
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	79 #if $imputation.imputation_method == "random"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	80 --meanPercentile '$imputation.meanPercentile'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	81 --sdPercentile '$imputation.sdPercentile'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	82 #end if
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	83 --regexSampleNames '$sample_names_regex_f'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	84 --regexSampleGrouping '$sample_grouping_regex_f'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	85 #if $group_filter.group_filter_method == "none"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	86 --sampleGroupFilter 'none'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	87 #else
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	88 --sampleGroupFilter '$group_filter.group_filter_method'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	89 --sampleGroupFilterPatterns '$group_filter_patterns_f'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	90 --sampleGroupFilterMode '$group_filter.group_filter_mode'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	91 #end if
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	92 --intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	93 --imputedDataFile '$imputed_data_file'
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	94 --imputedQNLTDataFile '$imp_qn_lt_file'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	95 --ksea_sqlite '$ksea_sqlite'
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	96 --kseaMinSubstrateCount '$ksea_min_substrate_count'
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	97 --ksea_cutoff_threshold '$ksea_cutoff_threshold'
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	98 --ksea_cutoff_statistic 'FDR'
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	99 --kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc'
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	100 --minQuality '$ksea_min_quality'
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	101 --anova_ksea_metadata '$anova_ksea_metadata'
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	102 --reportFile '$report_file'
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	103 ]]></command>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	104 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	105 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	106 <configfiles>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	107 <configfile name="sample_names_regex_f">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	108 $sample_names_regex
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	109 </configfile>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	110 <configfile name="sample_grouping_regex_f">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	111 $sample_grouping_regex
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	112 </configfile>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	113 <configfile name="group_filter_patterns_f">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	114 #if $group_filter.group_filter_method != "none"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	115 $group_filter.group_filter_patterns
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	116 #end if
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	117 </configfile>
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	118 <configfile name="intensity_column_regex_f">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	119 $intensity_column_regex
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	120 </configfile>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	121 </configfiles>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	122 <inputs>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	123 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	124 needed inputs:
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	125 - # should filters be used to identify sample-groups to be included or excluded
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	126 sampleGroupFilter: !r c("none", "exclude", "include")[3]
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	127 - # what patterns should be used to match sample-groups
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	128 # (extracted by regexSampleGrouping) when determining sample-groups
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	129 # that should be included or excluded
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	130 sampleGroupFilterPatterns: ".CR,N."
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	131 - # minimum number of observed values per class
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	132 intensityMinPerClass: 0
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	133 - # what should be the primary criterion to eliminate excessive heatmap rows
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	134 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	135 suggested or advanced inputs:
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	136 - kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	137 - kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	138 -->
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	139 <param name="input_file" type="data" format="tabular" label="Filtered phosphopeptide intensities (tabular)"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	140 help="'preproc_tab' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	141 />
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	142 <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level (tabular)"
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	143 help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	144 />
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	145 <param name="preproc_sqlite" type="data" format="sqlite" label="Database from mqppep_preproc (sqlite)"
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	146 help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	147 />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	148 <param name="intensity_column_regex" type="text" value="^Intensity[^_]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	149 label="Intensity-column pattern"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	150 help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	151 />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	152 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	153 <conditional name="imputation">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	154 <param name="imputation_method" type="select" label="Imputation method"
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	155 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 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	156 >
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	157 <option value="random" selected="true">random</option>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	158 <option value="group-median">group-median</option>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	159 <option value="median">median</option>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	160 <option value="mean">mean</option>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	161 </param>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	162 <when value="group-median" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	163 <when value="median" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	164 <when value="mean" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	165 <when value="random">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	166 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	167 label="Mean percentile for random values"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	168 help="Percentile center of random values; range [1,99]"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	169 />
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	170 <param name="sdPercentile" type="float" value="1"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	171 label="Percentile SD for random values"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	172 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 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	173 />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	174 </when>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	175 </conditional>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	176 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	177 help="Pattern extracting sample-names from names of columns of 'Filtered phosphopeptide intensities' that have peptide intensity data (PERL-compatible regular expression)"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	178 label="Sample-name extraction pattern">
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	179 <sanitizer>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	180 <valid initial="string.printable">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	181 <remove value="'"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	182 </valid>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	183 </sanitizer>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	184 </param>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	185 <param name="sample_grouping_regex" type="text" value="\d+"
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	186 help="Pattern extracting sample-group from the extracted sample-names (PERL-compatible regular expression)"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	187 label="Sample-group extraction pattern">
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	188 <sanitizer>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	189 <valid initial="string.printable">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	190 <remove value="'"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	191 </valid>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	192 </sanitizer>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	193 </param>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	194 <param name="intnsty_min_vals_per_smpl_grp" type="integer" value="1" min="0"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	195 label="Minimum number of values per sample-group"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	196 help="Only consider as comparable those intensities having at least this number of values in each sample-group (range [0,∞])"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	197 />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	198 <conditional name="group_filter">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	199 <param name="group_filter_method" type="select" label="Filter sample-groups"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	200 help="What filter should be applied to sample-group names? (1) 'none', no filter; (2) 'include', match is required; (3) 'exclude', match is forbidden."
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	201 >
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	202 <option value="none" selected="true">none</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	203 <option value="include">include</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	204 <option value="exclude">exclude</option>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	205 </param>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	206 <when value="none" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	207 <when value="include">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	208 <expand macro="group_matching_parm"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	209 </when>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	210 <when value="exclude">
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	211 <expand macro="group_matching_parm"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	212 </when>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	213 </conditional>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	214 <param name="ksea_min_substrate_count" type="integer" value="1" min="1"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	215 label="Minimum number of kinase-substrates for KSEA"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	216 help="Minimum number of substrates to consider any kinase for KSEA (range [1,∞])"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	217 />
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	218 <param name="ksea_cutoff_threshold" type="float" value="0.05"
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	219 label="KSEA threshold level"
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	220 help="Maximum FDR to be used to score a kinase enrichment as significant; see warning against setting this too low in help text below."
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	221 />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	222 <param name="ksea_use_absolute_log2_fc"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	223 type="boolean"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	224 label="Use abs(log2(fold-change)) for KSEA"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	225 help="Should log2(fold-change) be used for KSEA? (Checking this may alter (possibly reduce) the number of hits.)"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	226 checked="false"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	227 truevalue="TRUE"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	228 falsevalue="FALSE"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	229 />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	230 <param name="ksea_min_quality" type="integer" value="0" min="0"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	231 label="Minimum quality of substrates for KSEA"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	232 help="Minimum 'quality' of substrates to be considered for KSEA (range [0,∞]); higher numbers reduce the number of substrates considered - see help text below."
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	233 />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	234 </inputs>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	235 <outputs>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	236 <!-- earlier outputs will appear lower in the history list; therefore, put report at the top -->
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	237 <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	238 <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	239 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	240 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" />
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	241 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" />
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	242 </outputs>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	243 <tests>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	244 <test><!-- test #1 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	245 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	246 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	247 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	248 <param name="intensity_column_regex" value="^Intensity[^_]"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	249 <param name="imputation_method" value="median"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	250 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	251 <param name="sample_grouping_regex" value="\d+"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	252 <output name="imputed_data_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	253 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	254 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	255 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	256 <!-- missing missing observd missing observd observd -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	257 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	258
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	259 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	260 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	261 <output name="imp_qn_lt_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	262 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	263 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	264 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	265 <!-- missing missing observed missing observed observed -->
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	266 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.962256.6.908828.6.814580.6.865411.6.908828.7.093748" />
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	267
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	268 <has_text text="pSQKQEEENPAEETGEEK" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	269 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	270 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	271 </test>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	272 <test><!-- test #2 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	273 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	274 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	275 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	276 <param name="intensity_column_regex" value="^Intensity[^_]"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	277 <param name="imputation_method" value="mean"/>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	278 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	279 <param name="meanPercentile" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	280 <param name="sdPercentile" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	281 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	282 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	283 <param name="sample_grouping_regex" value="\d+"/>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	284 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	285 <param name="group_filter_method" value="none"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	286 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	287 <param name="group_filter_mode" value="r"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	288 <param name="group_filter_patterns" value="\.+"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	289 -->
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	290 <param name="ksea_min_substrate_count" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	291 <param name="ksea_cutoff_threshold" value="0.5"/>
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	292 <output name="imputed_data_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	293 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	294 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	295 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	296 <!-- missing missing observd missing observd observd -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	297 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	298
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	299 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	300 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	301 <output name="imp_qn_lt_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	302 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	303 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	304 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	305 <!-- missing missing observed missing observed observed -->
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	306 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.839850.6.797424.6.797424.6.797424.6.896609.7.097251" />
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	307 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	308 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	309 </test>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	310 <test><!-- test #3 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	311 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	312 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	313 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	314 <param name="intensity_column_regex" value="^Intensity[^_]"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	315 <param name="imputation_method" value="group-median"/>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	316 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	317 <param name="meanPercentile" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	318 <param name="sdPercentile" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	319 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	320 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	321 <param name="sample_grouping_regex" value="\d+"/>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	322 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	323 <param name="group_filter_method" value="none"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	324 <!--
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	325 <param name="group_filter_mode" value="r"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	326 <param name="group_filter_patterns" value="\.+"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	327 -->
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	328 <param name="ksea_min_substrate_count" value="1"/>
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	329 <param name="ksea_cutoff_threshold" value="0.5"/>
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	330 <output name="imputed_data_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	331 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	332 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	333 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	334 <!-- missing missing observd missing observd observd -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	335 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	336
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	337 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	338 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	339 <output name="imp_qn_lt_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	340 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	341 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	342 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	343 <!-- missing missing observed missing observed observed -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	344 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.946112.6.888985.6.792137.6.792137.6.888985.7.089555" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	345 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	346 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	347 </test>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	348 <test><!-- test #4 -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	349 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	350 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	351 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	352 <param name="intensity_column_regex" value="^Intensity[^_]"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	353 <param name="imputation_method" value="random"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	354 <param name="meanPercentile" value="1" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	355 <param name="sdPercentile" value="1.0" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	356 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	357 <param name="sample_grouping_regex" value="\d+"/>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	358 <output name="imputed_data_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	359 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	360 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	361 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	362 <!-- observd observd observd -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	363 <has_text_matching expression="pSQKQEEENPAEETGEEK.8765300.2355900.*4706000" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	364
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	365 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	366 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	367 <output name="imp_qn_lt_file">
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	368 <assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	369 <has_text text="Phosphopeptide" />
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	370 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	371 <has_text text="5.522821" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B -->
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	372 <has_text text="6.638251" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A -->
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	373 </assert_contents>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	374 </output>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	375 </test>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	376 </tests>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	377 <help><![CDATA[
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	378 ====================================================
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	379 Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	380 ====================================================
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	381
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	382 Overview
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	383 ============
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	384
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	385 Perform statistical analysis of preprocessed MaxQuant output data collected as described in `[Cheng, 2018] <https://doi.org/10.3791/57996>`_.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	386
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	387 - Extracts sample-group IDs from sample names.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	388 - Imputes missing values.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	389 - Performs ANOVA analysis for each phosphopeptide.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	390 - Performs Kinase-Substrate Enrichment Analysis (KSEA) using the method described by `Casado et al. (2013) <doi:10.1126/scisignal.2003573>`_; see "Algorithms" section below.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	391
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	392 Workflow position
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	393 =====================
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	394
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	395 Upstream tool
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	396 The "MaxQuant Phosphopeptide Preprocessing" tool (``mqppep_preproc``) that transforms MaxQuant output for phospoproteome-enriched samples into a form suitable for statistical analysis.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	397
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	398 Input datasets
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	399 ==================
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	400
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	401 ``Filtered phosphopeptide intensities`` (tabular)
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	402 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	403 This is the output from the "MaxQuant Phopsphopeptide Preprocessing"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	404 (``mqppep_preproc``) tool.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	405
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	406 - First column label 'Phosphopeptide'.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	407 - Sample-intensities must begin in first column matching 'Intensity-column pattern' and must have column labels to match argument 'Sample-name extraction pattern'.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	408
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	409 ``ANOVA alpha cutoff level`` (tabular)
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	410 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	411
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	412 ::
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	413
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	414 0.2
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	415 0.1
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	416 0.05
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	417
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	418 ``Database from mqppep_preproc`` (sqlite)
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	419 SQLite database produced by the "MaxQuant Phopsphopeptide Preprocessing"
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	420 (``mqppep_preproc``) tool.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	421
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	422 Input parameters
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	423 ====================
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	424
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	425 ``Intensity-column pattern``
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	426 First column of ``Filtered phosphopeptide intensities`` having intensity values (integer or PERL-compatible regular expression matching column label). Default::
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	427
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	428 ^Intensity[^_]
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	429
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	430 ``Imputation method``
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	431 Impute missing values by:
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	432
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	433 1. ``group-median`` - use median for each sample-group;
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	434 2. ``mean`` - use mean across all samples; or
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	435 3. ``median`` - use median across all samples;
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	436 4. ``random`` - use randomly generated values where:
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	437
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	438 (i) ``Mean percentile for random values`` specifies the percentile among non-missing values to be used as mean of random values, and
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	439 (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.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	440
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	441 ``Sample-name extraction pattern``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	442 PERL-compatible regular expression extracting the sample-name from the the name of a column of intensities (from ``Filtered phosphopeptide intensities``) for one sample.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	443
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	444 - For example, ``"\.\d+[A-Z]$"`` applied to "``Intensity.splunge.10A``" would produce "``.10A``".
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	445 - Note that this is case sensitive by default.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	446
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	447 ``Sample-group extraction pattern``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	448 PERL-compatible regular expression extracting the sample-grouping from the sample-name (that was in turn extracted with ``Sample-name extraction pattern`` from a column of intensites from ``Filtered phosphopeptide intensities``).
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	449
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	450 - For example, ``"\d+$"`` applied to "``.10A``" would produce "``10``".
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	451 - Note that this is case sensitive by default.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	452
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	453 ``Minimum number of values per sample-group``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	454 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 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	455
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	456 ``Filter sample-groups``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	457 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").
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	458
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	459 ``Sample-group matching mode``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	460 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.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	461
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	462 ``Sample-group matching pattern``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	463 This is a comma-separated list of patterns to match to group-names, according to the ``Sample-group matching mode`` that you have chosen.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	464
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	465 ``Minimum number of kinase-substrates for KSEA``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	466 For KSEA, you may decide that you wish to ignore kinases having fewer substrates than some minimum; specify that minimum here (range [1,]]>∞<![CDATA[])
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	467
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	468 ``KSEA threshold level``
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	469 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.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	470
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	471 ``Use abs(log2(fold-change)) for KSEA``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	472 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.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	473
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	474 ``Minimum quality of substrates for KSEA``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	475 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 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	476
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	477 Outputs
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	478 ===========
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	479
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	480 Report dataset
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	481 [input file].[imputation method]-``imputed_report``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	482
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	483 Summary report for normalization, imputation, and ANOVA, in PDF format.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	484
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	485 Imputed intensities
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	486 [input file].[imputation method]-``imputed_intensities``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	487
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	488 Phosphopeptide MS intensities where missing values have been imputed by the chosen method, in tabular format.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	489
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	490 Imputed quantum-normalized log-transformed intensities
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	491 [input file].[imputation method]-``imputed_QN_LT_intensities``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	492
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	493 Phosphopeptide MS intensities where missing values have been imputed by the chosen method, quantile-normalized (QN), and log10-transformed (LT), in tabular format.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	494
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	495 ANOVA KSEA metadata
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	496 [input file].[imputation method]-``imputed_anova_ksea_metadata``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	497 Phosphopeptide metadata including ANOVA significance and KSEA enrichments.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	498
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	499 KSEA SQLite database sqlite
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	500 [input file].[imputation method]-``imputed_ksea_sqlite``
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	501 An SQLite database that is usable for ad hoc report creation.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	502
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	503 Algorithm
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	504 =============
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	505
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	506 The KSEA algorithm used here is as in the KSEAapp package as reported in `[Wiredja 2017] <https://doi.org/10.1093/bioinformatics/btx415>`_.
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	507 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.
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	508
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	509 Authors
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	510 ===========
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	511
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	512 ``Larry C. Cheng``
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	513 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	514
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	515 ``Arthur C. Eschenlauer``
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	516 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	517
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	518 ===================================
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	519 PERL-compatible regular expressions
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	520 ===================================
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	521
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	522 Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	523
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	524 ]]></help>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	525 <citations>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	526 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	527 <citation type="doi">10.3791/57996</citation>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	528 <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 -->
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	529 <citation type="doi">10.1093/bioinformatics/btx415</citation>
1 2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	530 <citation type="bibtex">@Manual{,
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	531 title = {KSEAapp: Kinase-Substrate Enrichment Analysis},
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	532 author = {Danica D. Wiredja},
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	533 year = {2017},
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	534 note = {R package version 0.99.0},
2276e88d5a1f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be galaxyp parents: 0 diff changeset	535 }</citation>
0 d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	536 </citations>
d9b68bedbc91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe galaxyp parents: diff changeset	537 </tool>

Mercurial > repos > galaxyp > mqppep_anova

annotate mqppep_anova.xml @ 5:7d1f8a256cf6 draft default tip