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annotate mqppep_anova.xml @ 29:42b207aaa527 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 83864e12abbf63728a389b7fe677f3b88844e03f
author eschen42
date Thu, 27 Oct 2022 22:11:38 +0000
parents 5b8e15b2a67c
children 8ff2c287ff1c
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1 <tool
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2 id="mqppep_anova"
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3 name="MaxQuant Phosphopeptide ANOVA"
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4 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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5 profile="21.05"
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6 >
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7 <description>Runs ANOVA and KSEA for phosphopeptides.</description>
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8 <macros>
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9 <import>macros.xml</import>
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10 <xml name="group_matching_parm">
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11 <param name="group_filter_mode" type="select"
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12 help="Regular expression matching mode 'fixed', 'perl', or 'grep' with option for case insensitivity. See https://rdrr.io/r/base/grep.html"
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13 label="Sample-group matching mode"
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14 >
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15 <option value="r" selected="true">ERE ("extended regular expressions")</option>
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16 <option value="ri"> - ERE, case insensitive</option>
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17 <option value="p">PCRE ("PERL-compatible regular expressions")</option>
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18 <option value="pi"> - PCRE, case insensitive</option>
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19 <option value="f">fixed strings ("no regular expressions")</option>
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20 <option value="fi"> - fixed strings, case insensitive</option>
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21 </param>
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22 <param name="group_filter_patterns" type="text" value="\.+"
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23 help="Comma-separated list of regular expressions matching group-names"
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24 label="Sample-group matching pattern">
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25 <sanitizer>
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26 <valid initial="string.printable">
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27 <remove value="&apos;"/>
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28 </valid>
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29 </sanitizer>
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30 </param>
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31 </xml>
0
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32 </macros>
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33 <edam_topics>
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34 <edam_topic>topic_0121</edam_topic><!-- proteomics -->
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35 <edam_topic>topic_3520</edam_topic><!-- proteomics experiment-->
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36 </edam_topics>
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37 <edam_operations>
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38 <edam_operation>operation_0276</edam_operation><!-- Analyse a network of protein interactions. -->
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39 <edam_operation>operation_0531</edam_operation><!-- Heat map generation -->
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40 <edam_operation>operation_2938</edam_operation><!-- Dendrogram generation -->
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41 <edam_operation>operation_2938</edam_operation><!-- Imputation -->
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42 <edam_operation>operation_3435</edam_operation><!-- Standardisation and normalisation -->
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43 <edam_operation>operation_3501</edam_operation><!-- Enrichment analysis -->
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44 <edam_operation>operation_3658</edam_operation><!-- Statistical inference -->
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45 </edam_operations>
7
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46 <expand macro="requirements"/>
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47 <!--
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48 The weird invocation used here is because knitr and install_tinytex
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49 both need access to a writeable directory, but most directories in a
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50 biocontainer are read-only, so this builds a pseudo-home under /tmp
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51 -->
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52 <command detect_errors="exit_code"><![CDATA[
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53 (printenv | sort) &&
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54 cp '$__tool_directory__/mqppep_anova_script.Rmd' . &&
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55 cp '$__tool_directory__/mqppep_anova.R' . &&
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56 cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . &&
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57 cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . &&
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58 cp '$__tool_directory__/mqppep_anova_preamble.tex' . &&
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59 cp '$__tool_directory__/perpage.tex' . &&
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60 cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . &&
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61 Rscript mqppep_anova.R
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62 --inputFile '$input_file'
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63 --alphaFile '$alpha_file'
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64 --preproc_sqlite '$preproc_sqlite'
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65 --firstDataColumn '$intensity_column_regex_f'
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66 --imputationMethod $imputation.imputation_method
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67 #if $imputation.imputation_method == "random"
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68 --meanPercentile '$imputation.meanPercentile'
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69 --sdPercentile '$imputation.sdPercentile'
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70 #end if
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71 --regexSampleNames '$sample_names_regex_f'
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72 --regexSampleGrouping '$sample_grouping_regex_f'
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73 #if $group_filter.group_filter_method == "none"
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74 --sampleGroupFilter 'none'
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75 #else
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76 --sampleGroupFilter '$group_filter.group_filter_method'
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77 --sampleGroupFilterPatterns '$group_filter_patterns_f'
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78 --sampleGroupFilterMode '$group_filter.group_filter_mode'
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79 #end if
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80 --intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp'
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81 --imputedDataFile '$imputed_data_file'
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82 --imputedQNLTDataFile '$imp_qn_lt_file'
22
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83 --ksea_sqlite '$ksea_sqlite'
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84 --kseaMinSubstrateCount '$ksea_min_substrate_count'
22
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85 --ksea_cutoff_threshold '$ksea_cutoff_threshold'
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86 --ksea_cutoff_statistic 'FDR'
26
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87 --kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc'
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88 --minQuality '$ksea_min_quality'
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89 --anova_ksea_metadata '$anova_ksea_metadata'
26
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90 --reportFile '$report_file'
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91 ]]></command>
26
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92 <!--
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93 -->
0
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94 <configfiles>
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95 <configfile name="sample_names_regex_f">
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96 $sample_names_regex
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97 </configfile>
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98 <configfile name="sample_grouping_regex_f">
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99 $sample_grouping_regex
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100 </configfile>
26
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101 <configfile name="group_filter_patterns_f">
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102 #if $group_filter.group_filter_method != "none"
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103 $group_filter.group_filter_patterns
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104 #end if
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105 </configfile>
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106 <configfile name="intensity_column_regex_f">
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107 $intensity_column_regex
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108 </configfile>
0
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109 </configfiles>
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110 <inputs>
26
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111 <!--
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112 needed inputs:
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113 - # should filters be used to identify sample-groups to be included or excluded
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114 sampleGroupFilter: !r c("none", "exclude", "include")[3]
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115 - # what patterns should be used to match sample-groups
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116 # (extracted by regexSampleGrouping) when determining sample-groups
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117 # that should be included or excluded
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118 sampleGroupFilterPatterns: ".*CR,N.*"
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119 - # minimum number of observed values per class
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120 intensityMinPerClass: 0
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121 - # what should be the primary criterion to eliminate excessive heatmap rows
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122 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
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123 suggested or advanced inputs:
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124 - kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
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125 - kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
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126 -->
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127 <param name="input_file" type="data" format="tabular" label="Filtered phosphopeptide intensities (tabular)"
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128 help="'preproc_tab' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
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129 />
26
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130 <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level (tabular)"
22
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131 help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header"
0
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132 />
26
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133 <param name="preproc_sqlite" type="data" format="sqlite" label="Database from mqppep_preproc (sqlite)"
22
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134 help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
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135 />
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136 <param name="intensity_column_regex" type="text" value="^Intensity[^_]"
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137 label="Intensity-column pattern"
22
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138 help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)"
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139 />
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140 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
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141 <conditional name="imputation">
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142 <param name="imputation_method" type="select" label="Imputation method"
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143 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')"
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144 >
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145 <option value="random" selected="true">random</option>
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146 <option value="group-median">group-median</option>
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147 <option value="median">median</option>
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148 <option value="mean">mean</option>
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149 </param>
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150 <when value="group-median" />
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151 <when value="median" />
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152 <when value="mean" />
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153 <when value="random">
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154 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
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155 label="Mean percentile for random values"
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156 help="Percentile center of random values; range [1,99]"
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157 />
26
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158 <param name="sdPercentile" type="float" value="1"
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159 label="Percentile SD for random values"
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160 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.)"
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161 />
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162 </when>
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163 </conditional>
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164 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
26
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165 help="Pattern extracting sample-names from names of columns of 'Filtered phosphopeptide intensities' that have peptide intensity data (PERL-compatible regular expression)"
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166 label="Sample-name extraction pattern">
0
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167 <sanitizer>
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168 <valid initial="string.printable">
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169 <remove value="&apos;"/>
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170 </valid>
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171 </sanitizer>
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172 </param>
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173 <param name="sample_grouping_regex" type="text" value="\d+"
26
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174 help="Pattern extracting sample-group from the extracted sample-names (PERL-compatible regular expression)"
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175 label="Sample-group extraction pattern">
0
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176 <sanitizer>
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177 <valid initial="string.printable">
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178 <remove value="&apos;"/>
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179 </valid>
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180 </sanitizer>
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181 </param>
26
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182 <param name="intnsty_min_vals_per_smpl_grp" type="integer" value="1" min="0"
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183 label="Minimum number of values per sample-group"
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184 help="Only consider as comparable those intensities having at least this number of values in each sample-group (range [0,&#8734;])"
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185 />
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186 <conditional name="group_filter">
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187 <param name="group_filter_method" type="select" label="Filter sample-groups"
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188 help="What filter should be applied to sample-group names? (1) 'none', no filter; (2) 'include', match is required; (3) 'exclude', match is forbidden."
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189 >
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190 <option value="none" selected="true">none</option>
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191 <option value="include">include</option>
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192 <option value="exclude">exclude</option>
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193 </param>
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194 <when value="none" />
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195 <when value="include">
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196 <expand macro="group_matching_parm"/>
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197 </when>
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198 <when value="exclude">
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199 <expand macro="group_matching_parm"/>
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200 </when>
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201 </conditional>
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202 <param name="ksea_min_substrate_count" type="integer" value="1" min="1"
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203 label="Minimum number of kinase-substrates for KSEA"
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204 help="Minimum number of substrates to consider any kinase for KSEA (range [1,&#8734;])"
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205 />
22
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206 <param name="ksea_cutoff_threshold" type="float" value="0.05"
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207 label="KSEA threshold level"
26
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208 help="Maximum FDR to be used to score a kinase enrichment as significant; see warning against setting this too low in help text below."
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209 />
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210 <param name="ksea_use_absolute_log2_fc"
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211 type="boolean"
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212 label="Use abs(log2(fold-change)) for KSEA"
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213 help="Should log2(fold-change) be used for KSEA? (Checking this may alter (possibly reduce) the number of hits.)"
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214 checked="false"
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215 truevalue="TRUE"
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216 falsevalue="FALSE"
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217 />
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218 <param name="ksea_min_quality" type="integer" value="0" min="0"
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219 label="Minimum quality of substrates for KSEA"
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220 help="Minimum 'quality' of substrates to be considered for KSEA (range [0,&#8734;]); higher numbers reduce the number of substrates considered - see help text below."
22
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221 />
0
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222 </inputs>
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223 <outputs>
26
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224 <!-- earlier outputs will appear lower in the history list; therefore, put report at the top -->
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225 <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite" />
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226 <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" />
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227 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" />
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228 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" />
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229 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" />
0
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230 </outputs>
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231 <tests>
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232 <test><!-- test #1 -->
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233 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
22
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234 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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235 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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236 <param name="intensity_column_regex" value="^Intensity[^_]"/>
22
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237 <param name="imputation_method" value="median"/>
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238 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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239 <param name="sample_grouping_regex" value="\d+"/>
22
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240 <output name="imputed_data_file">
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241 <assert_contents>
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242 <has_text text="Phosphopeptide" />
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243 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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244 <!-- missing missing observd missing observd observd -->
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245 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" />
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246
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247 </assert_contents>
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248 </output>
13
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249 <output name="imp_qn_lt_file">
0
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250 <assert_contents>
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251 <has_text text="Phosphopeptide" />
5
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252 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
22
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253 <!-- missing missing observed missing observed observed -->
26
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254 <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
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255
5
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256 <has_text text="pSQKQEEENPAEETGEEK" />
0
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257 </assert_contents>
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258 </output>
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259 </test>
26
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260 <test><!-- test #2 -->
0
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261 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
22
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262 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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263 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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264 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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265 <param name="imputation_method" value="mean"/>
26
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266 <!--
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267 <param name="meanPercentile" value="1"/>
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268 <param name="sdPercentile" value="1"/>
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269 -->
22
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270 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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271 <param name="sample_grouping_regex" value="\d+"/>
26
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272 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
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273 <param name="group_filter_method" value="none"/>
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274 <!--
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275 <param name="group_filter_mode" value="r"/>
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276 <param name="group_filter_patterns" value="\.+"/>
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277 -->
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278 <param name="ksea_min_substrate_count" value="1"/>
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279 <param name="ksea_cutoff_threshold" value="0.5"/>
22
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280 <output name="imputed_data_file">
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281 <assert_contents>
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282 <has_text text="Phosphopeptide" />
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283 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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284 <!-- missing missing observd missing observd observd -->
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285 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" />
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286
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287 </assert_contents>
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288 </output>
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289 <output name="imp_qn_lt_file">
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290 <assert_contents>
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291 <has_text text="Phosphopeptide" />
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292 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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293 <!-- missing missing observed missing observed observed -->
26
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294 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.839850.*6.797424.*6.797424.*6.797424.*6.896609.*7.097251" />
22
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295 </assert_contents>
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296 </output>
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297 </test>
26
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298 <test><!-- test #3 -->
22
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299 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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300 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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301 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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302 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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303 <param name="imputation_method" value="group-median"/>
26
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304 <!--
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305 <param name="meanPercentile" value="1"/>
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306 <param name="sdPercentile" value="1"/>
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307 -->
22
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308 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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309 <param name="sample_grouping_regex" value="\d+"/>
26
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310 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
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311 <param name="group_filter_method" value="none"/>
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312 <!--
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313 <param name="group_filter_mode" value="r"/>
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314 <param name="group_filter_patterns" value="\.+"/>
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315 -->
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316 <param name="ksea_min_substrate_count" value="1"/>
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317 <param name="ksea_cutoff_threshold" value="0.5"/>
22
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318 <output name="imputed_data_file">
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319 <assert_contents>
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320 <has_text text="Phosphopeptide" />
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321 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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322 <!-- missing missing observd missing observd observd -->
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323 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" />
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324
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325 </assert_contents>
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326 </output>
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327 <output name="imp_qn_lt_file">
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328 <assert_contents>
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329 <has_text text="Phosphopeptide" />
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330 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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331 <!-- missing missing observed missing observed observed -->
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332 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.946112.*6.888985.*6.792137.*6.792137.*6.888985.*7.089555" />
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333 </assert_contents>
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334 </output>
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335 </test>
26
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336 <test><!-- test #4 -->
22
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337 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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338 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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339 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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340 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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341 <param name="imputation_method" value="random"/>
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342 <param name="meanPercentile" value="1" />
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343 <param name="sdPercentile" value="1.0" />
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344 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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345 <param name="sample_grouping_regex" value="\d+"/>
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346 <output name="imputed_data_file">
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347 <assert_contents>
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348 <has_text text="Phosphopeptide" />
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349 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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350 <!-- observd observd observd -->
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351 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.*2355900.*4706000" />
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352
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353 </assert_contents>
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354 </output>
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355 <output name="imp_qn_lt_file">
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356 <assert_contents>
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357 <has_text text="Phosphopeptide" />
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358 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
26
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359 <has_text text="5.522821" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B -->
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360 <has_text text="6.638251" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A -->
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361 </assert_contents>
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362 </output>
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363 </test>
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364 </tests>
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365 <help><![CDATA[
22
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366 ====================================================
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367 Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA
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368 ====================================================
0
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369
26
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370 **Overview**
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371 ============
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372
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373 Perform statistical analysis of preprocessed MaxQuant output data collected as described in `[Cheng, 2018] <https://doi.org/10.3791/57996>`_.
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374
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375 - Extracts sample-group IDs from sample names.
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376 - Imputes missing values.
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377 - Performs ANOVA analysis for each phosphopeptide.
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378 - Performs Kinase-Substrate Enrichment Analysis (KSEA) using the method described by `Casado et al. (2013) <doi:10.1126/scisignal.2003573>`_; see *"Algorithms"* section below.
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379
26
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380 **Workflow position**
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381 =====================
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382
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383 Upstream tool
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384 The "MaxQuant Phosphopeptide Preprocessing" tool (``mqppep_preproc``) that transforms MaxQuant output for phospoproteome-enriched samples into a form suitable for statistical analysis.
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385
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386 **Input datasets**
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387 ==================
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388
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389 ``Filtered phosphopeptide intensities`` (tabular)
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390 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
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391 This is the output from the "MaxQuant Phopsphopeptide Preprocessing"
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392 (``mqppep_preproc``) tool.
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393
26
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394 - First column label 'Phosphopeptide'.
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395 - Sample-intensities must begin in first column matching 'Intensity-column pattern' and must have column labels to match argument 'Sample-name extraction pattern'.
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396
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397 ``ANOVA alpha cutoff level`` (tabular)
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398 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
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399
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400 ::
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401
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402 0.2
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403 0.1
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404 0.05
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405
26
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406 ``Database from mqppep_preproc`` (sqlite)
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407 SQLite database produced by the "MaxQuant Phopsphopeptide Preprocessing"
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408 (``mqppep_preproc``) tool.
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409
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410 **Input parameters**
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411 ====================
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412
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413 ``Intensity-column pattern``
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414 First column of ``Filtered phosphopeptide intensities`` having intensity values (integer or PERL-compatible regular expression matching column label). Default::
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415
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416 ^Intensity[^_]
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417
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418 ``Imputation method``
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419 Impute missing values by:
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420
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421 1. ``group-median`` - use median for each sample-group;
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422 2. ``mean`` - use mean across all samples; or
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423 3. ``median`` - use median across all samples;
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424 4. ``random`` - use randomly generated values where:
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425
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426 (i) ``Mean percentile for random values`` specifies the percentile among non-missing values to be used as mean of random values, and
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427 (ii) ``Percentile SD for random values`` specifies the factor to be multiplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values.
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428
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429 ``Sample-name extraction pattern``
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430 PERL-compatible regular expression extracting the sample-name from the the name of a column of intensities (from ``Filtered phosphopeptide intensities``) for one sample.
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431
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432 - For example, ``"\.\d+[A-Z]$"`` applied to "``Intensity.splunge.10A``" would produce "``.10A``".
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433 - Note that *this is case sensitive* by default.
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434
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435 ``Sample-group extraction pattern``
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436 PERL-compatible regular expression extracting the sample-grouping from the sample-name (that was in turn extracted with ``Sample-name extraction pattern`` from a column of intensites from ``Filtered phosphopeptide intensities``).
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437
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438 - For example, ``"\d+$"`` applied to "``.10A``" would produce "``10``".
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439 - Note that *this is case sensitive* by default.
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440
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441 ``Minimum number of values per sample-group``
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442 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,]]>&#8734;<![CDATA[])
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443
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444 ``Filter sample-groups``
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445 Sometimes you may have spectra that are for treatments that you are not considering for your comparison. You can specify a filter (or not) for sample-group names; if you do, you can specify whether groups that match your criteria should be excluded from the analysis ("forbidden") or included in the analysis ("required").
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446
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447 ``Sample-group matching mode``
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448 The R `base::grep` function that is used here for pattern matching is exhaustively documented at https://rdrr.io/r/base/grep.html. There are two choices you make here. The first is whether to differentiate lowercase and uppercase characters. The second is wheter to require exact matches ("fixed" pattern-matching mode) or to use "PERL-compatible regular expressions) ("perl") or "extendd regular expressions" ("grep"). See https://rdrr.io/r/base/grep.html for further info.
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449
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450 ``Sample-group matching pattern``
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451 This is a comma-separated list of patterns to match to group-names, according to the ``Sample-group matching mode`` that you have chosen.
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452
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453 ``Minimum number of kinase-substrates for KSEA``
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454 For KSEA, you may decide that you wish to ignore kinases having fewer substrates than some minimum; specify that minimum here (range [1,]]>&#8734;<![CDATA[])
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455
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456 ``KSEA threshold level``
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457 Specifies minimum FDR at which a kinase will be considered to be enriched; the default choice of ``0.05`` is arbitrary and may exclude kinases that are interesting. The KSEA FDR perhaps should not be treated as conservatively as would be appropriate for hypothesis testing. For example, at an FDR of ``0.05``, for every ``20`` kinases that on discards, ``19`` are likely truely enriched.
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458
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459 ``Use abs(log2(fold-change)) for KSEA``
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460 When TRUE, consider only the magnitude of the differences across the contrast for all of the substrates when aggregating them to assess the enrichment of a given kinase's substrates. When FALSE, also consider the direction. Surprisingly, setting this to TRUE may decrease the enriched kinases.
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461
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462 ``Minimum quality of substrates for KSEA``
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463 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.
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464
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465 **Outputs**
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466 ===========
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467
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468 Report dataset
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469 *[input file].[imputation method]*-``imputed_report``
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470
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471 Summary report for normalization, imputation, and **ANOVA**, in PDF format.
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472
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473 Imputed intensities
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474 *[input file].[imputation method]*-``imputed_intensities``
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475
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476 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, in tabular format.
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477
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478 Imputed quantum-normalized log-transformed intensities
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479 *[input file].[imputation method]*-``imputed_QN_LT_intensities``
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480
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481 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, quantile-normalized (**QN**), and log10-transformed (**LT**), in tabular format.
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482
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483 ANOVA KSEA metadata
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484 *[input file].[imputation method]*-``imputed_anova_ksea_metadata``
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485 Phosphopeptide metadata including ANOVA significance and KSEA enrichments.
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486
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487 KSEA SQLite database sqlite
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488 *[input file].[imputation method]*-``imputed_ksea_sqlite``
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489 An SQLite database that is usable for *ad hoc* report creation.
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490
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491 **Algorithm**
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492 =============
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493
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494 The KSEA algorithm used here is as in the KSEAapp package as reported in `[Wiredja 2017] <https://doi.org/10.1093/bioinformatics/btx415>`_.
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495 The code is adapted from `"Danica D. Wiredja (2017). KSEAapp: Kinase-Substrate Enrichment Analysis. R package version 0.99.0." <https://cran.r-project.org/package=KSEAapp>`_ to work with output from the "MaxQuant Phosphopeptide Preprocessing" Galaxy tool and the multiple kinase-substrate databases that the latter tool searches.
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496
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497 **Authors**
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498 ===========
0
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499
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500 ``Larry C. Cheng``
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501 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
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502
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503 ``Arthur C. Eschenlauer``
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504 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
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505
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506 ===================================
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507 PERL-compatible regular expressions
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508 ===================================
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509
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510 Note that the PERL-compatible regular expressions accepted by this tool are documented at http://rdrr.io/r/base/regex.html
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511
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512 ]]></help>
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513 <citations>
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514 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
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515 <citation type="doi">10.3791/57996</citation>
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516 <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 -->
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517 <citation type="doi">10.1093/bioinformatics/btx415</citation>
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518 <citation type="bibtex">@Manual{,
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519 title = {KSEAapp: Kinase-Substrate Enrichment Analysis},
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520 author = {Danica D. Wiredja},
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521 year = {2017},
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522 note = {R package version 0.99.0},
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523 }</citation>
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524 </citations>
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525 </tool>