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annotate mqppep_anova.xml @ 3:f9c13bc8e7ad draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182-dirty"
author eschen42
date Mon, 07 Mar 2022 19:26:06 +0000
parents c1403d18c189
children d4d531006735
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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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1 <tool id="mqppep_anova" name="MaxQuant Phosphopeptide ANOVA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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2 <description>Perform ANOVA on merged and filtered data from phospho-peptide enrichment/MaxQuant pipeline</description>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.7.1">r-optparse</requirement>
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8 <requirement type="package" version="1.4.0">r-stringr</requirement>
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9 <requirement type="package" version="1.14.2">r-data.table</requirement>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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10 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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11 <requirement type="package" version="1.56.0">bioconductor-preprocesscore</requirement>
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12 <requirement type="package" version="0.3.3" >openblas</requirement>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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13 <requirement type="package" version="2.11" >r-rmarkdown</requirement>
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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14 <requirement type="package" version="0.4.0" >r-sass</requirement>
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15 <requirement type="package" >texlive-core</requirement>
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16
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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17 </requirements>
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18 <!-- Rscript -e 'rmarkdown::render("QuantDataProcessingScript.Rmd")' -->
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19 <command detect_errors="exit_code"><![CDATA[
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20 cat $sample_names_regex_f; cat $sample_grouping_regex_f;
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21 Rscript '$__tool_directory__/mqppep_anova.R'
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22 --inputFile '$input_file'
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23 --alphaFile $alpha_file
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24 --firstDataColumn $first_data_column
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25 --imputationMethod $imputation.imputation_method
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26 #if '$imputation_method' == 'random':
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27 --meanPercentile '$meanPercentile'
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28 --sdPercentile '$sdPercentile'
c1403d18c189 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit bb6c941be50db4c0719efdeaa904d7cb7aa1d182"
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29 #end if
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30 --regexSampleNames $sample_names_regex_f
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31 --regexSampleGrouping $sample_grouping_regex_f
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32 --imputedDataFile $imputed_data_file
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33 --reportFile $report_file
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34 ]]></command>
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35 <configfiles>
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36 <configfile name="sample_names_regex_f">
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37 $sample_names_regex
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38 </configfile>
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39 <configfile name="sample_grouping_regex_f">
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40 $sample_grouping_regex
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41 </configfile>
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42 </configfiles>
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43 <inputs>
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44 <param name="input_file" type="data" format="tabular" label="Filtered Phosphopeptide Intensities"
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45 help="[input_file] Phosphopeptide intensities filtered for minimal quality. First column label 'Phosphopeptide'; sample-intensities must begin in column 10 and must have column labels to match argument [sample_names_regex]"
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46 />
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47 <param name="alpha_file" type="data" format="tabular" label="alpha cutoff level"
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48 help="[alpha_file] List of alpha cutoff values for significance testing; text file having one column and no header"
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49 />
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50 <param name="first_data_column" type="text" value="Intensity"
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51 label="First data column"
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52 help="[first_data_column] First column having intensity values (integer or PERL-compatible regular expression matching column label)"
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53 />
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54 <!-- imputation_method <- c("group-median","median","mean","random")[1] -->
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55 <conditional name="imputation">
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56 <param name="imputation_method" type="select" label="Imputation Method"
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57 help="[imputation_method] 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 std. dev. as across all samples (with mean specified by [meanPercentile])"
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58 >
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59 <option value="random" selected="true">random</option>
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60 <option value="group-median">group-median</option>
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61 <option value="median">median</option>
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62 <option value="mean">mean</option>
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63 </param>
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64 <when value="group-median" />
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65 <when value="median" />
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66 <when value="mean" />
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67 <when value="random">
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68 <param name="meanPercentile" type="integer" value="1" min="1" max="99"
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69 label="Mean percentile for random values"
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70 help="[meanPercentile] Percentile center of random values; range [1,99]"
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71 />
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72 <param name="sdPercentile" type="float" value="0.2"
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73 label="Percentile std. dev. for random values"
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74 help="[sdPercentile] Standard deviation adjustment-factor for random values; real number. (1.0 means SD equal to the SD for the entire data set.)"
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75 />
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76 </when>
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77 </conditional>
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78 <param name="sample_names_regex" type="text" value="\.(\d+)[A-Z]$"
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79 help="[sample_names_regex] PERL-compatible regular expression extracting sample-names from the the name of a spectrum file (without extension)"
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80 label="Sample-extraction regex">
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81 <sanitizer>
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82 <valid initial="string.printable">
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83 <remove value="&apos;"/>
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84 </valid>
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85 </sanitizer>
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86 </param>
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87 <param name="sample_grouping_regex" type="text" value="(\d+)"
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88 help="[sample_grouping_regex] PERL-compatible regular expression extracting sample-group from each sample-name (i.e., extracted by previous regex pattern)"
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89 label="Group-extraction regex">
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90 <sanitizer>
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91 <valid initial="string.printable">
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92 <remove value="&apos;"/>
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93 </valid>
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94 </sanitizer>
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95 </param>
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96 </inputs>
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97 <outputs>
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98 <data name="imputed_data_file" format="tabular" label="${input_file.name}.intensities_${imputation.imputation_method}-imputed_QN_LT" ></data>
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99 <data name="report_file" format="html" label="${input_file.name}.report (download/unzip to view)" ></data>
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100 </outputs>
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101 <tests>
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102 <test>
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103 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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104 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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105 <param name="first_data_column" value="10"/>
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106 <param name="imputation_method" value="group-median"/>
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107 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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108 <param name="sample_grouping_regex" value="\d+"/>
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109 <output name="imputed_data_file">
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110 <assert_contents>
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111 <has_text text="Phosphopeptide" />
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112 <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" />
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113 <has_text text="23574000" />
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114 <has_text text="pSESELIDELSEDFDR" />
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115 </assert_contents>
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116 </output>
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117 </test>
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118 <test>
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119 <param name="input_file" ftype="tabular" value="test_input_for_anova.tabular"/>
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120 <param name="alpha_file" ftype="tabular" value="alpha_levels.tabular"/>
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121 <param name="first_data_column" value="10"/>
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122 <param name="imputation_method" value="random"/>
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123 <param name="sample_names_regex" value="\.\d+[A-Z]$"/>
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124 <param name="sample_grouping_regex" value="\d+"/>
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125 <output name="imputed_data_file">
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126 <assert_contents>
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127 <has_text text="Phosphopeptide" />
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128 <has_text text="AAAAAAAGDpSDpSWDADAFSVEDPVRK" />
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129 <has_text text="997800000" />
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130 <has_text text="pSESELIDELSEDFDR" />
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131 </assert_contents>
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132 </output>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 ===========================================
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137 Phopsphoproteomic Enrichment Pipeline ANOVA
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138 ===========================================
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139
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140 **Input files**
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141
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142 ``input_file``
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143 Phosphopeptides annotated with SwissProt and phosphosite metadata (in tabular format).
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144 This is the output from the "Phopsphoproteomic Enrichment Pipeline Merge and Filter"
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145 (``mqppep_mrgflt``) tool.
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146
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147 ``alpha_file``
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148 List of alpha cutoff values for significance testing; text file having one column and no header. For example:
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149
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150 ::
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151
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152 0.2
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153 0.1
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154 0.05
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155
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156 **Input parameters**
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157
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158 ``first_data_column``
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159 First column of ``input_file`` having intensity values (integer or PERL-compatible regular expression matching column label). Default: **Intensity**
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160
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161 ``imputation_method``
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162 Impute missing values by:
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163
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164 1. using median for each sample-group;
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165 2. using median across all samples;
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166 3. using mean across all samples; or
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167 4. using randomly generated values where:
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168
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169 - ``meanPercentile`` specifies the percentile among non-missing values to be used as mean of random values, and
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170 - ``sdPercentile`` specifies the factor to be mulitplied by the standard deviation among the non-missing values (across all samples) to determine the standard deviation of random values.
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171
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172 ``sample_names_regex``
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173 PERL-compatible regular expression extracting the sample-name from the the name of a column of instensities (from ``input_file``) for one sample.
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174
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175 - For example, ``"\.\d+[A-Z]$"`` applied to ``Intensity.splunge.10A`` would produce ``.10A``
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176 - Note that *this is case sensitive* by default.
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177
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178 ``sample_grouping_regex``
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179 PERL-compatible regular expression extracting the sample-grouping from the sample-name that was extracted with ``sample_names_regex`` from a column of intensites (from ``input_file``).
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180
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181 - For example, ``"\d+$"`` applied to ``.10A`` would produce ``10``
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182 - Note that *this is case sensitive* by default.
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183
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184
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185 **Outputs**
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186
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187 ``intensities_*-imputed_QN_LT``
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188 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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189
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190 ``report_file``
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191 (download/unzip to view) Summary report for normalization, imputation, and ANOVA.
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192 This dataset is displayed in Galaxy as having a datatype of ``html`` in Galaxy,
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193 but it is in fact a zipfile; the zip file contains
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194 an HTML file. Please download and unzip it locally to view the report.
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195 Ideally this report would be a PDF, but there is an issue
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196 `(linked here)
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197 <https://github.com/conda-forge/texlive-core-feedstock/issues/19>`_.
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198 that needs to be resolved first.
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199
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200 **Authors**
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201
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202 ``Larry C. Cheng``
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203 (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script.
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204
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205 ``Arthur C. Eschenlauer``
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206 (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
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207
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208 ===================================
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209 PERL-compatible regular expressions
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210 ===================================
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211
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212 Note that the PERL-compatible regular expressions accepted by this tool are documented at https://rdrr.io/r/base/regex.html
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213
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214 ]]></help>
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215 <citations>
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216 <!-- Cheng_2018 "Phosphopeptide Enrichment ..." PMID: 30124664 -->
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217 <citation type="doi">10.3791/57996</citation>
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218 </citations>
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219 </tool>