mqppep_anova: mqppep_anova.xml annotate

annotate mqppep_anova.xml @ 31:c33c30398908 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9

author	eschen42
date	Fri, 09 Dec 2022 21:05:54 +0000
parents	8ff2c287ff1c
children	f61fa0dd6b06

rev	line source
16 2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	1 <tool
2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	2 id="mqppep_anova"
2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	3 name="MaxQuant Phosphopeptide ANOVA"
2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	5 profile="21.05"
2b9119d7d80a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7127d1511d45a8b22d4f50eee6db24d844371227" eschen42 parents: 15 diff changeset	6 >
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	7 <description>Runs ANOVA and KSEA for phosphopeptides.</description>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	8 <macros>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	9 <import>macros.xml</import>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	10 <xml name="group_matching_parm">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	11 <param name="group_filter_mode" type="select"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 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"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	13 label="Sample-group matching mode"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	14 >
30 8ff2c287ff1c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 34795323c4d2e2b49e7d07c0119ba0b2c7c0a720 eschen42 parents: 26 diff changeset	15 <option value="r">ERE ("extended regular expressions")</option>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	16 <option value="ri"> - ERE, case insensitive</option>
30 8ff2c287ff1c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 34795323c4d2e2b49e7d07c0119ba0b2c7c0a720 eschen42 parents: 26 diff changeset	17 <option value="p" selected="true">PCRE ("PERL-compatible regular expressions")</option>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	18 <option value="pi"> - PCRE, case insensitive</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	19 <option value="f">fixed strings ("no regular expressions")</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	20 <option value="fi"> - fixed strings, case insensitive</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	21 </param>
30 8ff2c287ff1c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 34795323c4d2e2b49e7d07c0119ba0b2c7c0a720 eschen42 parents: 26 diff changeset	22 <param name="group_filter_patterns" type="text" value=".+"
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	23 help="Comma-separated list of regular expressions matching group-names"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	24 label="Sample-group matching pattern">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	25 <sanitizer>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	26 <valid initial="string.printable">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	27 <remove value="'"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	28 </valid>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	29 </sanitizer>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	30 </param>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	31 </xml>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	32 </macros>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	33 <edam_topics>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	34 <edam_topic>topic_0121</edam_topic><!-- proteomics -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	35 <edam_topic>topic_3520</edam_topic><!-- proteomics experiment-->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	36 </edam_topics>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	37 <edam_operations>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	38 <edam_operation>operation_0276</edam_operation><!-- Analyse a network of protein interactions. -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	39 <edam_operation>operation_0531</edam_operation><!-- Heat map generation -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	40 <edam_operation>operation_2938</edam_operation><!-- Dendrogram generation -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	41 <edam_operation>operation_2938</edam_operation><!-- Imputation -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	42 <edam_operation>operation_3435</edam_operation><!-- Standardisation and normalisation -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	43 <edam_operation>operation_3501</edam_operation><!-- Enrichment analysis -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	44 <edam_operation>operation_3658</edam_operation><!-- Statistical inference -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	45 </edam_operations>
7 d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	46 <expand macro="requirements"/>
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	47 <!--
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	48 The weird invocation used here is because knitr and install_tinytex
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	49 both need access to a writeable directory, but most directories in a
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	50 biocontainer are read-only, so this builds a pseudo-home under /tmp
d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	51 -->
31 c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	52 <required_files>
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	53 <include path="KSEA_impl_flowchart.pdf" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	54 <include path="kinase_name_uniprot_lut.tabular.bz2" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	55 <include path="kinase_uniprot_description_lut.tabular.bz2" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	56 <include path="kinase_uniprot_description_lut.tabular.bz2" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	57 <include path="mqppep_anova.R" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	58 <include path="mqppep_anova_preamble.tex" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	59 <include path="mqppep_anova_script.Rmd" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	60 <include path="perpage.tex" />
c33c30398908 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 7e8b616a2519c8faeb6fd743a8fb73f271f655f9 eschen42 parents: 30 diff changeset	61 </required_files>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	62 <command detect_errors="exit_code"><![CDATA[
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	63 (printenv \| sort) &&
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	64 cp '$__tool_directory__/mqppep_anova_script.Rmd' . &&
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	65 cp '$__tool_directory__/mqppep_anova.R' . &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	66 cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	67 cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	68 cp '$__tool_directory__/mqppep_anova_preamble.tex' . &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	69 cp '$__tool_directory__/perpage.tex' . &&
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	70 cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . &&
17 bb38aac026b9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aea9ac5a98069c3c993bd7903eda732f8ae2109d" eschen42 parents: 16 diff changeset	71 Rscript mqppep_anova.R
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	72 --inputFile '$input_file'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	73 --alphaFile '$alpha_file'
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	74 --preproc_sqlite '$preproc_sqlite'
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	75 --firstDataColumn '$intensity_column_regex_f'
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	76 --imputationMethod $imputation.imputation_method
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	77 #if $imputation.imputation_method == "random"
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	78 --meanPercentile '$imputation.meanPercentile'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	79 --sdPercentile '$imputation.sdPercentile'
b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	80 #end if
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	81 --regexSampleNames '$sample_names_regex_f'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	82 --regexSampleGrouping '$sample_grouping_regex_f'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	83 #if $group_filter.group_filter_method == "none"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	84 --sampleGroupFilter 'none'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	85 #else
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	86 --sampleGroupFilter '$group_filter.group_filter_method'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	87 --sampleGroupFilterPatterns '$group_filter_patterns_f'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	88 --sampleGroupFilterMode '$group_filter.group_filter_mode'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	89 #end if
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	90 --intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	91 --imputedDataFile '$imputed_data_file'
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	92 --imputedQNLTDataFile '$imp_qn_lt_file'
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	93 --ksea_sqlite '$ksea_sqlite'
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	94 --kseaMinSubstrateCount '$ksea_min_substrate_count'
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	95 --ksea_cutoff_threshold '$ksea_cutoff_threshold'
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	96 --ksea_cutoff_statistic 'FDR'
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	97 --kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc'
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	98 --minQuality '$ksea_min_quality'
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	99 --anova_ksea_metadata '$anova_ksea_metadata'
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	100 --reportFile '$report_file'
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	101 ]]></command>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	102 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	103 -->
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	104 <configfiles>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	105 <configfile name="sample_names_regex_f">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	106 $sample_names_regex
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	107 </configfile>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	108 <configfile name="sample_grouping_regex_f">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	109 $sample_grouping_regex
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	110 </configfile>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	111 <configfile name="group_filter_patterns_f">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	112 #if $group_filter.group_filter_method != "none"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	113 $group_filter.group_filter_patterns
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	114 #end if
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	115 </configfile>
15 2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	116 <configfile name="intensity_column_regex_f">
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	117 $intensity_column_regex
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	118 </configfile>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	119 </configfiles>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	120 <inputs>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	121 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	122 needed inputs:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	123 - # should filters be used to identify sample-groups to be included or excluded
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	124 sampleGroupFilter: !r c("none", "exclude", "include")[3]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	125 - # what patterns should be used to match sample-groups
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	126 # (extracted by regexSampleGrouping) when determining sample-groups
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	127 # that should be included or excluded
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	128 sampleGroupFilterPatterns: ".CR,N."
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	129 - # minimum number of observed values per class
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	130 intensityMinPerClass: 0
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	131 - # what should be the primary criterion to eliminate excessive heatmap rows
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	132 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	133 suggested or advanced inputs:
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	134 - kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	135 - kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	136 -->
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	137 <param name="input_file" type="data" format="tabular" label="Filtered phosphopeptide intensities (tabular)"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	138 help="'preproc_tab' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	139 />
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	140 <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level (tabular)"
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	141 help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	142 />
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	143 <param name="preproc_sqlite" type="data" format="sqlite" label="Database from mqppep_preproc (sqlite)"
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	144 help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	145 />
15 2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	146 <param name="intensity_column_regex" type="text" value="^Intensity[^_]"
2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	147 label="Intensity-column pattern"
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	148 help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	149 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	150 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	151 <conditional name="imputation">
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	152 <param name="imputation_method" type="select" label="Imputation method"
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	153 help="Impute missing values by (1) using median for each sample-group; (2) using median across all samples; (3) using mean across all samples; or (4) using randomly generated values having same SD as across all samples (with mean specified by 'Mean percentile for random values')"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	154 >
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	155 <option value="random" selected="true">random</option>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	156 <option value="group-median">group-median</option>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	157 <option value="median">median</option>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	158 <option value="mean">mean</option>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	159 </param>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	160 <when value="group-median" />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	161 <when value="median" />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	162 <when value="mean" />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	163 <when value="random">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	164 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	165 label="Mean percentile for random values"
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	166 help="Percentile center of random values; range [1,99]"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	167 />
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	168 <param name="sdPercentile" type="float" value="1"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	169 label="Percentile SD for random values"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	170 help="Standard deviation adjustment-factor for random values; real number. (1.0 means SD of random values equal to the SD for the entire data set.)"
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	171 />
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	172 </when>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	173 </conditional>
12 4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0" eschen42 parents: 7 diff changeset	174 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	175 help="Pattern extracting sample-names from names of columns of 'Filtered phosphopeptide intensities' that have peptide intensity data (PERL-compatible regular expression)"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	176 label="Sample-name extraction pattern">
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	177 <sanitizer>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	178 <valid initial="string.printable">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	179 <remove value="'"/>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	180 </valid>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	181 </sanitizer>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	182 </param>
12 4deacfee76ef "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e87d28ea433cc26db7fe44768685d08c06f7a0d0" eschen42 parents: 7 diff changeset	183 <param name="sample_grouping_regex" type="text" value="\d+"
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	184 help="Pattern extracting sample-group from the extracted sample-names (PERL-compatible regular expression)"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	185 label="Sample-group extraction pattern">
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	186 <sanitizer>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	187 <valid initial="string.printable">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	188 <remove value="'"/>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	189 </valid>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	190 </sanitizer>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	191 </param>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	192 <param name="intnsty_min_vals_per_smpl_grp" type="integer" value="1" min="0"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	193 label="Minimum number of values per sample-group"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	194 help="Only consider as comparable those intensities having at least this number of values in each sample-group (range [0,∞])"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	195 />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	196 <conditional name="group_filter">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	197 <param name="group_filter_method" type="select" label="Filter sample-groups"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	198 help="What filter should be applied to sample-group names? (1) 'none', no filter; (2) 'include', match is required; (3) 'exclude', match is forbidden."
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	199 >
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	200 <option value="none" selected="true">none</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	201 <option value="include">include</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	202 <option value="exclude">exclude</option>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	203 </param>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	204 <when value="none" />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	205 <when value="include">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	206 <expand macro="group_matching_parm"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	207 </when>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	208 <when value="exclude">
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	209 <expand macro="group_matching_parm"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	210 </when>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	211 </conditional>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	212 <param name="ksea_min_substrate_count" type="integer" value="1" min="1"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	213 label="Minimum number of kinase-substrates for KSEA"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	214 help="Minimum number of substrates to consider any kinase for KSEA (range [1,∞])"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	215 />
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	216 <param name="ksea_cutoff_threshold" type="float" value="0.05"
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	217 label="KSEA threshold level"
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	218 help="Maximum FDR to be used to score a kinase enrichment as significant; see warning against setting this too low in help text below."
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	219 />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	220 <param name="ksea_use_absolute_log2_fc"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	221 type="boolean"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	222 label="Use abs(log2(fold-change)) for KSEA"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	223 help="Should log2(fold-change) be used for KSEA? (Checking this may alter (possibly reduce) the number of hits.)"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	224 checked="false"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	225 truevalue="TRUE"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	226 falsevalue="FALSE"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	227 />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	228 <param name="ksea_min_quality" type="integer" value="0" min="0"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	229 label="Minimum quality of substrates for KSEA"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	230 help="Minimum 'quality' of substrates to be considered for KSEA (range [0,∞]); higher numbers reduce the number of substrates considered - see help text below."
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	231 />
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	232 </inputs>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	233 <outputs>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	234 <!-- earlier outputs will appear lower in the history list; therefore, put report at the top -->
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	235 <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite" />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	236 <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	237 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	238 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" />
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	239 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" />
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	240 </outputs>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	241 <tests>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	242 <test><!-- test #1 -->
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	243 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	244 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	245 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
15 2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	246 <param name="intensity_column_regex" value="^Intensity[^_]"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	247 <param name="imputation_method" value="median"/>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	248 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	249 <param name="sample_grouping_regex" value="\d+"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	250 <output name="imputed_data_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	251 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	252 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	253 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	254 <!-- missing missing observd missing observd observd -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	255 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	256
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	257 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	258 </output>
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	259 <output name="imp_qn_lt_file">
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	260 <assert_contents>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	261 <has_text text="Phosphopeptide" />
5 d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 0 diff changeset	262 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	263 <!-- missing missing observed missing observed observed -->
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	264 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.962256.6.908828.6.814580.6.865411.6.908828.7.093748" />
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	265
5 d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 0 diff changeset	266 <has_text text="pSQKQEEENPAEETGEEK" />
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	267 </assert_contents>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	268 </output>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	269 </test>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	270 <test><!-- test #2 -->
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	271 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	272 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	273 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	274 <param name="intensity_column_regex" value="^Intensity[^_]"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	275 <param name="imputation_method" value="mean"/>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	276 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	277 <param name="meanPercentile" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	278 <param name="sdPercentile" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	279 -->
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	280 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	281 <param name="sample_grouping_regex" value="\d+"/>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	282 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	283 <param name="group_filter_method" value="none"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	284 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	285 <param name="group_filter_mode" value="r"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	286 <param name="group_filter_patterns" value="\.+"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	287 -->
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	288 <param name="ksea_min_substrate_count" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	289 <param name="ksea_cutoff_threshold" value="0.5"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	290 <output name="imputed_data_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	291 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	292 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	293 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	294 <!-- missing missing observd missing observd observd -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	295 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	296
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	297 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	298 </output>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	299 <output name="imp_qn_lt_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	300 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	301 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	302 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	303 <!-- missing missing observed missing observed observed -->
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	304 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.839850.6.797424.6.797424.6.797424.6.896609.7.097251" />
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	305 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	306 </output>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	307 </test>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	308 <test><!-- test #3 -->
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	309 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	310 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	311 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	312 <param name="intensity_column_regex" value="^Intensity[^_]"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	313 <param name="imputation_method" value="group-median"/>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	314 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	315 <param name="meanPercentile" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	316 <param name="sdPercentile" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	317 -->
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	318 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	319 <param name="sample_grouping_regex" value="\d+"/>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	320 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	321 <param name="group_filter_method" value="none"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	322 <!--
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	323 <param name="group_filter_mode" value="r"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	324 <param name="group_filter_patterns" value="\.+"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	325 -->
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	326 <param name="ksea_min_substrate_count" value="1"/>
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	327 <param name="ksea_cutoff_threshold" value="0.5"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	328 <output name="imputed_data_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	329 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	330 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	331 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	332 <!-- missing missing observd missing observd observd -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	333 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	334
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	335 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	336 </output>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	337 <output name="imp_qn_lt_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	338 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	339 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	340 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	341 <!-- missing missing observed missing observed observed -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	342 <has_text_matching expression="pSQKQEEENPAEETGEEK.6.946112.6.888985.6.792137.6.792137.6.888985.7.089555" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	343 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	344 </output>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	345 </test>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	346 <test><!-- test #4 -->
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	347 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	348 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	349 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
15 2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	350 <param name="intensity_column_regex" value="^Intensity[^_]"/>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	351 <param name="imputation_method" value="random"/>
7 d728198f1ba5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9a0fa6d0f9aadc069a5551a54da6daf307885637" eschen42 parents: 5 diff changeset	352 <param name="meanPercentile" value="1" />
15 2c5f1a2fe16a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 96659062ea07ac43d139746b0d119f1ee020f9cd" eschen42 parents: 13 diff changeset	353 <param name="sdPercentile" value="1.0" />
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	354 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	355 <param name="sample_grouping_regex" value="\d+"/>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	356 <output name="imputed_data_file">
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	357 <assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	358 <has_text text="Phosphopeptide" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	359 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	360 <!-- observd observd observd -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	361 <has_text_matching expression="pSQKQEEENPAEETGEEK.8765300.2355900.*4706000" />
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	362
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	363 </assert_contents>
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	364 </output>
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	365 <output name="imp_qn_lt_file">
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	366 <assert_contents>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	367 <has_text text="Phosphopeptide" />
5 d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 0 diff changeset	368 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	369 <has_text text="5.522821" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B -->
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	370 <has_text text="6.638251" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A -->
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	371 </assert_contents>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	372 </output>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	373 </test>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	374 </tests>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	375 <help><![CDATA[
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	376 ====================================================
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	377 Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	378 ====================================================
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	379
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	380 Overview
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	381 ============
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	382
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	383 Perform statistical analysis of preprocessed MaxQuant output data collected as described in `[Cheng, 2018] <https://doi.org/10.3791/57996>`_.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	384
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	385 - Extracts sample-group IDs from sample names.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	386 - Imputes missing values.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	387 - Performs ANOVA analysis for each phosphopeptide.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	388 - Performs Kinase-Substrate Enrichment Analysis (KSEA) using the method described by `Casado et al. (2013) <doi:10.1126/scisignal.2003573>`_; see "Algorithms" section below.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	389
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	390 Workflow position
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	391 =====================
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	392
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	393 Upstream tool
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	394 The "MaxQuant Phosphopeptide Preprocessing" tool (``mqppep_preproc``) that transforms MaxQuant output for phospoproteome-enriched samples into a form suitable for statistical analysis.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	395
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	396 Input datasets
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	397 ==================
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	398
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	399 ``Filtered phosphopeptide intensities`` (tabular)
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	400 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	401 This is the output from the "MaxQuant Phopsphopeptide Preprocessing"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	402 (``mqppep_preproc``) tool.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	403
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	404 - First column label 'Phosphopeptide'.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	405 - Sample-intensities must begin in first column matching 'Intensity-column pattern' and must have column labels to match argument 'Sample-name extraction pattern'.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	406
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	407 ``ANOVA alpha cutoff level`` (tabular)
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	408 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	409
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	410 ::
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	411
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	412 0.2
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	413 0.1
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	414 0.05
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	415
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	416 ``Database from mqppep_preproc`` (sqlite)
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	417 SQLite database produced by the "MaxQuant Phopsphopeptide Preprocessing"
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	418 (``mqppep_preproc``) tool.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	419
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	420 Input parameters
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	421 ====================
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	422
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	423 ``Intensity-column pattern``
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	424 First column of ``Filtered phosphopeptide intensities`` having intensity values (integer or PERL-compatible regular expression matching column label). Default::
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	425
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	426 ^Intensity[^_]
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	427
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	428 ``Imputation method``
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	429 Impute missing values by:
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	430
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	431 1. ``group-median`` - use median for each sample-group;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	432 2. ``mean`` - use mean across all samples; or
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	433 3. ``median`` - use median across all samples;
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	434 4. ``random`` - use randomly generated values where:
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	435
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	436 (i) ``Mean percentile for random values`` specifies the percentile among non-missing values to be used as mean of random values, and
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	437 (ii) ``Percentile SD for random values`` specifies the factor to be multiplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	438
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	439 ``Sample-name extraction pattern``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	440 PERL-compatible regular expression extracting the sample-name from the the name of a column of intensities (from ``Filtered phosphopeptide intensities``) for one sample.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	441
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	442 - For example, ``"\.\d+[A-Z]$"`` applied to "``Intensity.splunge.10A``" would produce "``.10A``".
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	443 - Note that this is case sensitive by default.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	444
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	445 ``Sample-group extraction pattern``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	446 PERL-compatible regular expression extracting the sample-grouping from the sample-name (that was in turn extracted with ``Sample-name extraction pattern`` from a column of intensites from ``Filtered phosphopeptide intensities``).
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	447
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	448 - For example, ``"\d+$"`` applied to "``.10A``" would produce "``10``".
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	449 - Note that this is case sensitive by default.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	450
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	451 ``Minimum number of values per sample-group``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	452 Sometimes you may wish to filter out the intensities that are poorly represented among some sample groups because they complicate the comparison process. You can use this parameter to specify the minimum number of values in any sample-group (range [0,]]>∞<![CDATA[])
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	453
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	454 ``Filter sample-groups``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	455 Sometimes you may have spectra that are for treatments that you are not considering for your comparison. You can specify a filter (or not) for sample-group names; if you do, you can specify whether groups that match your criteria should be excluded from the analysis ("forbidden") or included in the analysis ("required").
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	456
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	457 ``Sample-group matching mode``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	458 The R `base::grep` function that is used here for pattern matching is exhaustively documented at https://rdrr.io/r/base/grep.html. There are two choices you make here. The first is whether to differentiate lowercase and uppercase characters. The second is wheter to require exact matches ("fixed" pattern-matching mode) or to use "PERL-compatible regular expressions) ("perl") or "extendd regular expressions" ("grep"). See https://rdrr.io/r/base/grep.html for further info.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	459
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	460 ``Sample-group matching pattern``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	461 This is a comma-separated list of patterns to match to group-names, according to the ``Sample-group matching mode`` that you have chosen.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	462
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	463 ``Minimum number of kinase-substrates for KSEA``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	464 For KSEA, you may decide that you wish to ignore kinases having fewer substrates than some minimum; specify that minimum here (range [1,]]>∞<![CDATA[])
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	465
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	466 ``KSEA threshold level``
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	467 Specifies minimum FDR at which a kinase will be considered to be enriched; the default choice of ``0.05`` is arbitrary and may exclude kinases that are interesting. The KSEA FDR perhaps should not be treated as conservatively as would be appropriate for hypothesis testing. For example, at an FDR of ``0.05``, for every ``20`` kinases that on discards, ``19`` are likely truely enriched.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	468
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	469 ``Use abs(log2(fold-change)) for KSEA``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	470 When TRUE, consider only the magnitude of the differences across the contrast for all of the substrates when aggregating them to assess the enrichment of a given kinase's substrates. When FALSE, also consider the direction. Surprisingly, setting this to TRUE may decrease the enriched kinases.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	471
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	472 ``Minimum quality of substrates for KSEA``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	473 An arbitrary "quality score" is assigned to each substrate, as described in the PDF report produced by the tool. This score takes into account both FDR-adjusted p-value and the number of missing values for each substrate. Setting the minimum to zero retains all substrates, which may be a large number.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	474
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	475 Outputs
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	476 ===========
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	477
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	478 Report dataset
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	479 [input file].[imputation method]-``imputed_report``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	480
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	481 Summary report for normalization, imputation, and ANOVA, in PDF format.
13 b41a077af3aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 040e4945da00a279cb60daae799fce9489f99c50" eschen42 parents: 12 diff changeset	482
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	483 Imputed intensities
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	484 [input file].[imputation method]-``imputed_intensities``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	485
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	486 Phosphopeptide MS intensities where missing values have been imputed by the chosen method, in tabular format.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	487
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	488 Imputed quantum-normalized log-transformed intensities
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	489 [input file].[imputation method]-``imputed_QN_LT_intensities``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	490
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	491 Phosphopeptide MS intensities where missing values have been imputed by the chosen method, quantile-normalized (QN), and log10-transformed (LT), in tabular format.
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	492
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	493 ANOVA KSEA metadata
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	494 [input file].[imputation method]-``imputed_anova_ksea_metadata``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	495 Phosphopeptide metadata including ANOVA significance and KSEA enrichments.
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	496
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	497 KSEA SQLite database sqlite
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	498 [input file].[imputation method]-``imputed_ksea_sqlite``
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	499 An SQLite database that is usable for ad hoc report creation.
23 3911581e639a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit b18713d25e7b260d6cdaf99fb216a4d1b3014c47 eschen42 parents: 22 diff changeset	500
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	501 Algorithm
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	502 =============
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	503
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	504 The KSEA algorithm used here is as in the KSEAapp package as reported in `[Wiredja 2017] <https://doi.org/10.1093/bioinformatics/btx415>`_.
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	505 The code is adapted from `"Danica D. Wiredja (2017). KSEAapp: Kinase-Substrate Enrichment Analysis. R package version 0.99.0." <https://cran.r-project.org/package=KSEAapp>`_ to work with output from the "MaxQuant Phosphopeptide Preprocessing" Galaxy tool and the multiple kinase-substrate databases that the latter tool searches.
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	506
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	507 Authors
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	508 ===========
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	509
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	510 ``Larry C. Cheng``
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	511 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	512
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	513 ``Arthur C. Eschenlauer``
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	514 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	515
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	516 ===================================
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	517 PERL-compatible regular expressions
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	518 ===================================
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	519
5 d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf" eschen42 parents: 0 diff changeset	520 Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	521
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	522 ]]></help>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	523 <citations>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	524 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	525 <citation type="doi">10.3791/57996</citation>
22 61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	526 <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 -->
61adb8801b73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b eschen42 parents: 17 diff changeset	527 <citation type="doi">10.1093/bioinformatics/btx415</citation>
26 5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	528 <citation type="bibtex">@Manual{,
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	529 title = {KSEAapp: Kinase-Substrate Enrichment Analysis},
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	530 author = {Danica D. Wiredja},
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	531 year = {2017},
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	532 note = {R package version 0.99.0},
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488 eschen42 parents: 23 diff changeset	533 }</citation>
0 c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	534 </citations>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182" eschen42 parents: diff changeset	535 </tool>

Mercurial > repos > eschen42 > mqppep_anova

annotate mqppep_anova.xml @ 31:c33c30398908 draft