Mercurial > repos > eschen42 > mqppep_anova

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 5a40fd5ab46727e07c20348f194813b69d582d24
author eschen42
date Mon, 27 Mar 2023 20:56:50 +0000
parents f61fa0dd6b06
children
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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>
0
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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">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" selected="true">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=".+"
26
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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>
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32 </macros>
22
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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 -->
32
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52 <!-- commenting out to appease linter
31
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53 <required_files>
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54 <include path="KSEA_impl_flowchart.pdf" />
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55 <include path="kinase_name_uniprot_lut.tabular.bz2" />
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56 <include path="kinase_uniprot_description_lut.tabular.bz2" />
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57 <include path="kinase_uniprot_description_lut.tabular.bz2" />
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58 <include path="mqppep_anova.R" />
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59 <include path="mqppep_anova_preamble.tex" />
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60 <include path="mqppep_anova_script.Rmd" />
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61 <include path="perpage.tex" />
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62 </required_files>
32
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63 -->
0
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64 <command detect_errors="exit_code"><![CDATA[
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65 (printenv | sort) &&
22
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66 cp '$__tool_directory__/mqppep_anova_script.Rmd' . &&
26
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67 cp '$__tool_directory__/mqppep_anova.R' . &&
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68 cp '$__tool_directory__/kinase_name_uniprot_lut.tabular.bz2' . &&
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69 cp '$__tool_directory__/kinase_uniprot_description_lut.tabular.bz2' . &&
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70 cp '$__tool_directory__/mqppep_anova_preamble.tex' . &&
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71 cp '$__tool_directory__/perpage.tex' . &&
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72 cp '$__tool_directory__/KSEA_impl_flowchart.pdf' . &&
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73 Rscript mqppep_anova.R
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74 --inputFile '$input_file'
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75 --alphaFile '$alpha_file'
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76 --preproc_sqlite '$preproc_sqlite'
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77 --firstDataColumn '$intensity_column_regex_f'
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78 --imputationMethod $imputation.imputation_method
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79 #if $imputation.imputation_method == "random"
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80 --meanPercentile '$imputation.meanPercentile'
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81 --sdPercentile '$imputation.sdPercentile'
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82 #end if
26
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83 --regexSampleNames '$sample_names_regex_f'
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84 --regexSampleGrouping '$sample_grouping_regex_f'
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85 #if $group_filter.group_filter_method == "none"
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86 --sampleGroupFilter 'none'
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87 #else
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88 --sampleGroupFilter '$group_filter.group_filter_method'
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89 --sampleGroupFilterPatterns '$group_filter_patterns_f'
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90 --sampleGroupFilterMode '$group_filter.group_filter_mode'
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91 #end if
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92 --intensityMinValuesPerClass '$intnsty_min_vals_per_smpl_grp'
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93 --imputedDataFile '$imputed_data_file'
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94 --imputedQNLTDataFile '$imp_qn_lt_file'
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95 --ksea_sqlite '$ksea_sqlite'
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96 --kseaMinSubstrateCount '$ksea_min_substrate_count'
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97 --ksea_cutoff_threshold '$ksea_cutoff_threshold'
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98 --ksea_cutoff_statistic 'FDR'
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99 --kseaUseAbsoluteLog2FC '$ksea_use_absolute_log2_fc'
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100 --minQuality '$ksea_min_quality'
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101 --anova_ksea_metadata '$anova_ksea_metadata'
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102 --reportFile '$report_file'
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103 ]]></command>
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104 <!--
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105 -->
0
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106 <configfiles>
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107 <configfile name="sample_names_regex_f">
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108 $sample_names_regex
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109 </configfile>
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110 <configfile name="sample_grouping_regex_f">
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111 $sample_grouping_regex
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112 </configfile>
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113 <configfile name="group_filter_patterns_f">
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114 #if $group_filter.group_filter_method != "none"
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115 $group_filter.group_filter_patterns
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116 #end if
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117 </configfile>
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118 <configfile name="intensity_column_regex_f">
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119 $intensity_column_regex
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120 </configfile>
0
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121 </configfiles>
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122 <inputs>
26
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123 <!--
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124 needed inputs:
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125 - # should filters be used to identify sample-groups to be included or excluded
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126 sampleGroupFilter: !r c("none", "exclude", "include")[3]
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127 - # what patterns should be used to match sample-groups
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128 # (extracted by regexSampleGrouping) when determining sample-groups
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129 # that should be included or excluded
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130 sampleGroupFilterPatterns: ".*CR,N.*"
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131 - # minimum number of observed values per class
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132 intensityMinPerClass: 0
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133 - # what should be the primary criterion to eliminate excessive heatmap rows
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134 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1]
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135 suggested or advanced inputs:
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136 - kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2"
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137 - kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2"
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138 -->
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139 <param name="input_file" type="data" format="tabular" label="Filtered phosphopeptide intensities (tabular)"
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140 help="'preproc_tab' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
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141 />
26
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142 <param name="alpha_file" type="data" format="tabular" label="ANOVA alpha cutoff level (tabular)"
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143 help="ANOVA alpha cutoff values for significance testing: tabular data having one column and no header"
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144 />
26
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145 <param name="preproc_sqlite" type="data" format="sqlite" label="Database from mqppep_preproc (sqlite)"
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146 help="'preproc_sqlite' dataset produced by 'MaxQuant Phosphopeptide Preprocessing' tool"
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147 />
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148 <param name="intensity_column_regex" type="text" value="^Intensity[^_]"
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149 label="Intensity-column pattern"
22
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150 help="Pattern matching columns that have peptide intensity data (PERL-compatible regular expression matching column label)"
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151 />
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152 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
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153 <conditional name="imputation">
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154 <param name="imputation_method" type="select" label="Imputation method"
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155 help="Impute missing values by (1) using median for each sample-group; (2) using median across all samples; (3) using mean across all samples; or (4) using randomly generated values having same SD as across all samples (with mean specified by 'Mean percentile for random values')"
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156 >
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157 <option value="random" selected="true">random</option>
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158 <option value="group-median">group-median</option>
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159 <option value="median">median</option>
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160 <option value="mean">mean</option>
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161 </param>
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162 <when value="group-median" />
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163 <when value="median" />
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164 <when value="mean" />
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165 <when value="random">
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166 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
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167 label="Mean percentile for random values"
22
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168 help="Percentile center of random values; range [1,99]"
0
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169 />
26
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170 <param name="sdPercentile" type="float" value="1"
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171 label="Percentile SD for random values"
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172 help="Standard deviation adjustment-factor for random values; real number. (1.0 means SD of random values equal to the SD for the entire data set.)"
0
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173 />
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174 </when>
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175 </conditional>
12
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176 <param name="sample_names_regex" type="text" value="\.\d+[A-Z]$"
26
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177 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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178 label="Sample-name extraction pattern">
0
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179 <sanitizer>
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180 <valid initial="string.printable">
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181 <remove value="&apos;"/>
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182 </valid>
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183 </sanitizer>
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184 </param>
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185 <param name="sample_grouping_regex" type="text" value="\d+"
26
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186 help="Pattern extracting sample-group from the extracted sample-names (PERL-compatible regular expression)"
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187 label="Sample-group extraction pattern">
0
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188 <sanitizer>
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189 <valid initial="string.printable">
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190 <remove value="&apos;"/>
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191 </valid>
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192 </sanitizer>
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193 </param>
26
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194 <param name="intnsty_min_vals_per_smpl_grp" type="integer" value="1" min="0"
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195 label="Minimum number of values per sample-group"
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196 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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197 />
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198 <conditional name="group_filter">
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199 <param name="group_filter_method" type="select" label="Filter sample-groups"
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200 help="What filter should be applied to sample-group names? (1) 'none', no filter; (2) 'include', match is required; (3) 'exclude', match is forbidden."
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201 >
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202 <option value="none" selected="true">none</option>
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203 <option value="include">include</option>
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204 <option value="exclude">exclude</option>
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205 </param>
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206 <when value="none" />
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207 <when value="include">
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208 <expand macro="group_matching_parm"/>
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209 </when>
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210 <when value="exclude">
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211 <expand macro="group_matching_parm"/>
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212 </when>
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213 </conditional>
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214 <param name="ksea_min_substrate_count" type="integer" value="1" min="1"
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215 label="Minimum number of kinase-substrates for KSEA"
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216 help="Minimum number of substrates to consider any kinase for KSEA (range [1,&#8734;])"
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217 />
22
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218 <param name="ksea_cutoff_threshold" type="float" value="0.05"
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219 label="KSEA threshold level"
26
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220 help="Maximum FDR to be used to score a kinase enrichment as significant; see warning against setting this too low in help text below."
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221 />
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222 <param name="ksea_use_absolute_log2_fc"
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223 type="boolean"
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224 label="Use abs(log2(fold-change)) for KSEA"
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225 help="Should log2(fold-change) be used for KSEA? (Checking this may alter (possibly reduce) the number of hits.)"
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226 checked="false"
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227 truevalue="TRUE"
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228 falsevalue="FALSE"
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229 />
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230 <param name="ksea_min_quality" type="integer" value="0" min="0"
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231 label="Minimum quality of substrates for KSEA"
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232 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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233 />
0
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234 </inputs>
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235 <outputs>
26
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236 <!-- earlier outputs will appear lower in the history list; therefore, put report at the top -->
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237 <data name="ksea_sqlite" format="sqlite" label="${input_file.name}..${imputation.imputation_method}-imputed_ksea_sqlite" />
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238 <data name="anova_ksea_metadata" format="tabular" label="${input_file.name}.${imputation.imputation_method}-anova_ksea_metadata" />
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239 <data name="imputed_data_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_intensities" />
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240 <data name="imp_qn_lt_file" format="tabular" label="${input_file.name}.${imputation.imputation_method}-imputed_QN_LT_intensities" />
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241 <data name="report_file" format="pdf" label="${input_file.name}.${imputation.imputation_method}-imputed_report" />
0
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242 </outputs>
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243 <tests>
26
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244 <test><!-- test #1 -->
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245 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
22
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246 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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247 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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248 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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249 <param name="imputation_method" value="median"/>
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250 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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251 <param name="sample_grouping_regex" value="\d+"/>
22
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252 <output name="imputed_data_file">
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253 <assert_contents>
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254 <has_text text="Phosphopeptide" />
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255 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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256 <!-- missing missing observd missing observd observd -->
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257 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.8765300.2355900.14706000" />
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258
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259 </assert_contents>
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260 </output>
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261 <output name="imp_qn_lt_file">
0
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262 <assert_contents>
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263 <has_text text="Phosphopeptide" />
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264 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
22
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265 <!-- missing missing observed missing observed observed -->
26
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266 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.962256.*6.908828.*6.814580.*6.865411.*6.908828.*7.093748" />
22
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267
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268 <has_text text="pSQKQEEENPAEETGEEK" />
0
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269 </assert_contents>
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270 </output>
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271 </test>
26
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272 <test><!-- test #2 -->
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273 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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274 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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275 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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276 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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277 <param name="imputation_method" value="mean"/>
26
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278 <!--
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279 <param name="meanPercentile" value="1"/>
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280 <param name="sdPercentile" value="1"/>
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281 -->
22
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282 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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283 <param name="sample_grouping_regex" value="\d+"/>
26
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284 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
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285 <param name="group_filter_method" value="none"/>
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286 <!--
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287 <param name="group_filter_mode" value="r"/>
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288 <param name="group_filter_patterns" value="\.+"/>
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289 -->
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290 <param name="ksea_min_substrate_count" value="1"/>
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291 <param name="ksea_cutoff_threshold" value="0.5"/>
22
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292 <output name="imputed_data_file">
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293 <assert_contents>
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294 <has_text text="Phosphopeptide" />
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295 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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296 <!-- missing missing observd missing observd observd -->
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297 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6721601.6721601.8765300.6721601.2355900.14706000" />
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298
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299 </assert_contents>
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300 </output>
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301 <output name="imp_qn_lt_file">
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302 <assert_contents>
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303 <has_text text="Phosphopeptide" />
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304 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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305 <!-- missing missing observed missing observed observed -->
26
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306 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.839850.*6.797424.*6.797424.*6.797424.*6.896609.*7.097251" />
22
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307 </assert_contents>
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308 </output>
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309 </test>
26
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310 <test><!-- test #3 -->
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311 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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312 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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313 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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314 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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315 <param name="imputation_method" value="group-median"/>
26
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316 <!--
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317 <param name="meanPercentile" value="1"/>
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318 <param name="sdPercentile" value="1"/>
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319 -->
22
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320 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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321 <param name="sample_grouping_regex" value="\d+"/>
26
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322 <param name="intnsty_min_vals_per_smpl_grp" value="1"/>
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323 <param name="group_filter_method" value="none"/>
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324 <!--
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325 <param name="group_filter_mode" value="r"/>
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326 <param name="group_filter_patterns" value="\.+"/>
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327 -->
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328 <param name="ksea_min_substrate_count" value="1"/>
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329 <param name="ksea_cutoff_threshold" value="0.5"/>
22
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330 <output name="imputed_data_file">
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331 <assert_contents>
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332 <has_text text="Phosphopeptide" />
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333 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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334 <!-- missing missing observd missing observd observd -->
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335 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.8765300.8765300.5886074.2355900.14706000" />
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336
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337 </assert_contents>
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338 </output>
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339 <output name="imp_qn_lt_file">
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340 <assert_contents>
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341 <has_text text="Phosphopeptide" />
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342 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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343 <!-- missing missing observed missing observed observed -->
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344 <has_text_matching expression="pSQKQEEENPAEETGEEK.*6.946112.*6.888985.*6.792137.*6.792137.*6.888985.*7.089555" />
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345 </assert_contents>
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346 </output>
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347 </test>
26
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348 <test><!-- test #4 -->
22
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349 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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350 <param name="preproc_sqlite" ftype="sqlite" value="test_input_for_anova.sqlite"/>
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351 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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352 <param name="intensity_column_regex" value="^Intensity[^_]"/>
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353 <param name="imputation_method" value="random"/>
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354 <param name="meanPercentile" value="1" />
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355 <param name="sdPercentile" value="1.0" />
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356 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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357 <param name="sample_grouping_regex" value="\d+"/>
22
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358 <output name="imputed_data_file">
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359 <assert_contents>
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360 <has_text text="Phosphopeptide" />
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361 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
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362 <!-- observd observd observd -->
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363 <has_text_matching expression="pSQKQEEENPAEETGEEK.*8765300.*2355900.*4706000" />
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364
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365 </assert_contents>
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366 </output>
13
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367 <output name="imp_qn_lt_file">
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368 <assert_contents>
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369 <has_text text="Phosphopeptide" />
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370 <has_text text="AAAITDMADLEELSRLpSPLPPGpSPGSAAR" />
26
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371 <has_text text="5.522821" /> <!-- log-transformed value for pTYVDPFTpYEDPNQAVR .1B -->
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372 <has_text text="6.638251" /> <!-- log-transformed value for pSQKQEEENPAEETGEEK .2A -->
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373 </assert_contents>
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374 </output>
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375 </test>
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376 </tests>
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377 <help><![CDATA[
22
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378 ====================================================
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379 Phopsphoproteomic Enrichment Pipeline ANOVA and KSEA
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380 ====================================================
0
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381
26
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382 **Overview**
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383 ============
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384
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385 Perform statistical analysis of preprocessed MaxQuant output data collected as described in `[Cheng, 2018] <https://doi.org/10.3791/57996>`_.
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386
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387 - Extracts sample-group IDs from sample names.
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388 - Imputes missing values.
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389 - Performs ANOVA analysis for each phosphopeptide.
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390 - Performs Kinase-Substrate Enrichment Analysis (KSEA) using the method described by `Casado et al. (2013) <doi:10.1126/scisignal.2003573>`_; see *"Algorithms"* section below.
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391
26
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392 **Workflow position**
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393 =====================
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394
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395 Upstream tool
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396 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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diff changeset
397
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398 **Input datasets**
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399 ==================
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400
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401 ``Filtered phosphopeptide intensities`` (tabular)
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402 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
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403 This is the output from the "MaxQuant Phopsphopeptide Preprocessing"
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404 (``mqppep_preproc``) tool.
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405
26
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406 - First column label 'Phosphopeptide'.
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407 - 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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408
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409 ``ANOVA alpha cutoff level`` (tabular)
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410 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
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411
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412 ::
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413
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414 0.2
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415 0.1
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416 0.05
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417
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418 ``Database from mqppep_preproc`` (sqlite)
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419 SQLite database produced by the "MaxQuant Phopsphopeptide Preprocessing"
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420 (``mqppep_preproc``) tool.
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421
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422 **Input parameters**
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423 ====================
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424
23
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425 ``Intensity-column pattern``
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426 First column of ``Filtered phosphopeptide intensities`` having intensity values (integer or PERL-compatible regular expression matching column label). Default::
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427
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428 ^Intensity[^_]
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429
23
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430 ``Imputation method``
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431 Impute missing values by:
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432
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433 1. ``group-median`` - use median for each sample-group;
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434 2. ``mean`` - use mean across all samples; or
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435 3. ``median`` - use median across all samples;
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436 4. ``random`` - use randomly generated values where:
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437
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438 (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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439 (ii) ``Percentile SD for random values`` specifies the factor to be multiplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values.
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440
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441 ``Sample-name extraction pattern``
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442 PERL-compatible regular expression extracting the sample-name from the the name of a column of intensities (from ``Filtered phosphopeptide intensities``) for one sample.
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443
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444 - For example, ``"\.\d+[A-Z]$"`` applied to "``Intensity.splunge.10A``" would produce "``.10A``".
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445 - Note that *this is case sensitive* by default.
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446
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447 ``Sample-group extraction pattern``
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448 PERL-compatible regular expression extracting the sample-grouping from the sample-name (that was in turn extracted with ``Sample-name extraction pattern`` from a column of intensites from ``Filtered phosphopeptide intensities``).
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449
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450 - For example, ``"\d+$"`` applied to "``.10A``" would produce "``10``".
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451 - Note that *this is case sensitive* by default.
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452
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453 ``Minimum number of values per sample-group``
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454 Sometimes you may wish to filter out the intensities that are poorly represented among some sample groups because they complicate the comparison process. You can use this parameter to specify the minimum number of values in any sample-group (range [0,]]>&#8734;<![CDATA[])
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455
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456 ``Filter sample-groups``
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457 Sometimes you may have spectra that are for treatments that you are not considering for your comparison. You can specify a filter (or not) for sample-group names; if you do, you can specify whether groups that match your criteria should be excluded from the analysis ("forbidden") or included in the analysis ("required").
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458
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459 ``Sample-group matching mode``
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460 The R `base::grep` function that is used here for pattern matching is exhaustively documented at https://rdrr.io/r/base/grep.html. There are two choices you make here. The first is whether to differentiate lowercase and uppercase characters. The second is wheter to require exact matches ("fixed" pattern-matching mode) or to use "PERL-compatible regular expressions) ("perl") or "extendd regular expressions" ("grep"). See https://rdrr.io/r/base/grep.html for further info.
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461
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462 ``Sample-group matching pattern``
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463 This is a comma-separated list of patterns to match to group-names, according to the ``Sample-group matching mode`` that you have chosen.
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464
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465 ``Minimum number of kinase-substrates for KSEA``
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466 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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467
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468 ``KSEA threshold level``
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469 Specifies minimum FDR at which a kinase will be considered to be enriched; the default choice of ``0.05`` is arbitrary and may exclude kinases that are interesting. The KSEA FDR perhaps should not be treated as conservatively as would be appropriate for hypothesis testing. For example, at an FDR of ``0.05``, for every ``20`` kinases that on discards, ``19`` are likely truely enriched.
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470
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471 ``Use abs(log2(fold-change)) for KSEA``
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472 When TRUE, consider only the magnitude of the differences across the contrast for all of the substrates when aggregating them to assess the enrichment of a given kinase's substrates. When FALSE, also consider the direction. Surprisingly, setting this to TRUE may decrease the enriched kinases.
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473
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474 ``Minimum quality of substrates for KSEA``
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475 An arbitrary "quality score" is assigned to each substrate, as described in the PDF report produced by the tool. This score takes into account both FDR-adjusted p-value and the number of missing values for each substrate. Setting the minimum to zero retains all substrates, which may be a large number.
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476
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477 **Outputs**
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478 ===========
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479
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480 Report dataset
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481 *[input file].[imputation method]*-``imputed_report``
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482
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483 Summary report for normalization, imputation, and **ANOVA**, in PDF format.
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484
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485 Imputed intensities
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486 *[input file].[imputation method]*-``imputed_intensities``
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487
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488 Phosphopeptide MS intensities where missing values have been **imputed** by the chosen method, in tabular format.
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489
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490 Imputed quantum-normalized log-transformed intensities
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491 *[input file].[imputation method]*-``imputed_QN_LT_intensities``
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492
5b8e15b2a67c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit e0b80550743f634282b4b4348b75e6f172dc1488
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493 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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c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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494
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495 ANOVA KSEA metadata
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496 *[input file].[imputation method]*-``imputed_anova_ksea_metadata``
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497 Phosphopeptide metadata including ANOVA significance and KSEA enrichments.
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498
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499 KSEA SQLite database sqlite
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500 *[input file].[imputation method]*-``imputed_ksea_sqlite``
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501 An SQLite database that is usable for *ad hoc* report creation.
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502
22
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503 **Algorithm**
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504 =============
22
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505
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506 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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507 The code is adapted from `"Danica D. Wiredja (2017). KSEAapp: Kinase-Substrate Enrichment Analysis. R package version 0.99.0." <https://cran.r-project.org/package=KSEAapp>`_ to work with output from the "MaxQuant Phosphopeptide Preprocessing" Galaxy tool and the multiple kinase-substrate databases that the latter tool searches.
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508
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509 **Authors**
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510 ===========
0
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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511
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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512 ``Larry C. Cheng``
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513 (`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"
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514
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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515 ``Arthur C. Eschenlauer``
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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516 (`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"
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517
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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518 ===================================
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519 PERL-compatible regular expressions
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520 ===================================
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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521
5
d4d531006735 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 92e8ab6fc27a1f02583742715d644bc96418fbdf"
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522 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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523
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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524 ]]></help>
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525 <citations>
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526 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
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527 <citation type="doi">10.3791/57996</citation>
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528 <!-- Wiredja_2017 "The KSEA App ..." PMID: 28655153 -->
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529 <citation type="doi">10.1093/bioinformatics/btx415</citation>
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530 <citation type="bibtex">@Manual{,
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531 title = {KSEAapp: Kinase-Substrate Enrichment Analysis},
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532 author = {Danica D. Wiredja},
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533 year = {2017},
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534 note = {R package version 0.99.0},
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535 }</citation>
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536 </citations>
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537 </tool>