Mercurial > repos > mbernt > proteomicsr_intensity_workflow

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty
author mbernt
date Tue, 19 Dec 2023 15:50:36 +0000
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31212f7e7611 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/proteomicsr commit a73787be689a9af5641ff1b594c9a35d29093247-dirty
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1 <macros>
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2 <token name="@TOOL_VERSION@">0.1.0</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">r-proteomicsr</requirement>
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7 <!-- <requirement type="package" version="2.58.0">bioconductor-biomart</requirement>
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8 <requirement type="package" version="4.10.0">bioconductor-clusterprofiler</requirement>
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9 <requirement type="package" version="1.24.0">bioconductor-dep</requirement>
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10 <requirement type="package" version="2.18.0">bioconductor-complexheatmap</requirement>
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11 <requirement type="package" version="1.20.0">bioconductor-kinswingr</requirement>
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12 <requirement type="package" version="0.4.15">r-circlize</requirement>
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13 <requirement type="package" version="3.4.0">r-classdiscovery</requirement>
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14 <requirement type="package" version="0.92">r-corrplot</requirement>
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15 <requirement type="package" version="0.3.4">r-dendsort</requirement>
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16 <requirement type="package" version="1.63_1">r-dynamictreecut</requirement>
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17 <requirement type="package" version="3.4.2">r-ggplot2</requirement>
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18 <requirement type="package" version="0.6.0">r-ggpubr</requirement>
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19 <requirement type="package" version="6.3.2">r-mixomics</requirement>
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20 <requirement type="package" version="7.5.1">r-msigdbr</requirement>
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21 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
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22 <requirement type="package" version="1.8.9">r-plyr</requirement>
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23 <requirement type="package" version="2.1.4">r-readr</requirement>
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24 <requirement type="package" version="1.4.4">r-reshape2</requirement>
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25 <requirement type="package" version="1.2.1">r-scales</requirement>
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26 <requirement type="package" version="1.4.8">r-splitstackshape</requirement>
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27 <requirement type="package" version="1.3.0">r-tidyr</requirement>
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28 <requirement type="package" version="1.71">r-wgcna</requirement>
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29 <requirement type="package" version="2.3.4">r-dbplyr</requirement> -->
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30
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31 <!-- conda create -y \-\-quiet \-\-strict-channel-priority \-\-solver libmamba \-\-override-channels \-\-channel conda-forge \-\-channel bioconda \-\-channel defaults \-\-name
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32 __r-proteomicsr@0.1.0
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33 "bioconductor-biomart=2.58.0" # needed update https://github.com/grimbough/biomaRt/issues/87
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34 "bioconductor-clusterprofiler=4.10.0" #(newer needed, otherwise conflict with bioconductor-biomart)
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35 "bioconductor-dep=1.24.0" # same
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36 bioconductor-complexheatmap=2.18.0
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37 bioconductor-kinswingr
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38 r-circlize=0.4.15
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39 r-classdiscovery=3.4.0
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40 r-corrplot=0.92 r-dendsort=0.3.4
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41 r-dynamictreecut=1.63_1
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42 r-ggplot2=3.4.2
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43 r-ggpubr=0.6.0
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44 r-mixomics=6.3.2
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45 r-msigdbr=7.5.1
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46 r-pheatmap=1.0.12
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47 r-plyr=1.8.9
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48 r-readr=2.1.4
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49 r-reshape2=1.4.4
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50 r-scales=1.2.1
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51 r-splitstackshape=1.4.8
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52 r-tidyr=1.3.0
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53 r-wgcna=1.71
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54 "r-dbplyr<2.4"
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55 -->
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56 <!-- <requirement type="package" version="3.0.0">r-ggsci</requirement> -->
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57 <!-- <requirement type="package" version="2.3">r-gridextra</requirement> -->
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58
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59 <yield/>
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60 </requirements>
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61 </xml>
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62
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63 <token name="@READ_INPUTS@"><![CDATA[
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64 #if $sampleTable.ext == 'csv'
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65 sampleTable <- read.csv("$sampleTable", row.names = 1)
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66 #else
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67 sampleTable <- read.delim("$sampleTable", header = TRUE, row.names = 1, sep = "\t")
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68 #end if
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69 @READ_SAMPLE_GENES_MAPPING@
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70 ]]></token>
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71
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72 <token name="@READ_SAMPLE_GENES_MAPPING@"><![CDATA[
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73 #if $sampleGenes
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74 #if $sampleGenes.ext == 'csv'
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75 sampleGenes <- read.csv("$sampleGenes", row.names = 1)
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76 #else
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77 sampleGenes <- read.delim("$sampleGenes", header = TRUE, row.names = 1, sep = "\t")
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78 #end if
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79 #else
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80 sampleGenes <- NULL
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81 #end if
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82 #if $sampleMapping
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83 #if $sampleMapping.ext == 'csv'
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84 sampleMapping <- read.csv("$sampleMapping", row.names = 1)
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85 #else
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86 sampleMapping <- read.delim("$sampleMapping", header = TRUE, row.names = 1, sep = "\t")
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87 #end if
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88 #else
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89 sampleMapping <- NULL
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90 #end if
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91 ]]></token>
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92
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93 <token name="@COMMON_WF_PARAMETERS@"><![CDATA[
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94 sampleTable,
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95 sampleGenes = sampleGenes, ## this implies more output data sets!
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96 sampleMapping = sampleMapping,
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97 remove_outliers = $remove_outliers,
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98 median_normalize = $median_normalize,
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99 number_replicates_reliable = $number_replicates_reliable,
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100 reliable_all_comparisons = $reliable_all_comparisons,
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101 alternative = "$alternative",
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102 var.equal = $var_equal,
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103 paired = $paired,
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104 pvalue_decision = "$pvalue_decision",
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105 pvalue_adjustment = "$pvalue_adjustment",
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106 significance_cutoff = $significance_cutoff,
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107 color_up = "${color_up}FF",
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108 color_none = "${color_none}FF",
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109 color_down = "${color_down}FF"
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110 ]]></token>
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111 <xml name="common_wf_paramerters">
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112 <param argument="sampleTable" type="data" format="csv,tabular" label="Sample table" help="Rows: unique identifiers (e.g. uniprot accessions), Columns: samples. Replicates should be indicated using _1, _2, .... Content should be numeric."/>
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113 <expand macro="sample_genes_mapping"/>
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114 <param argument="remove_outliers" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove outliers" help="Identified by the function identify_outliers() based on Mahalanobis distances"/>
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115 <param argument="median_normalize" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Apply median normalization" help=""/>
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116
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117 <yield/>
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118
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119 <param argument="number_replicates_reliable" type="integer" min="1" value="3" label="Number of replicates for reliable identification" help="Number of replicates for which quantitation data should be available to consider a protein reliably identified under the particular condition (i.e. in a sample)"/>
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120 <!--TODO formulation unclear, comparisons between what? Samples? -->
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121 <param argument="reliable_all_comparisons" type="select" label="Required comparisons" help="Candidates are returned that are identified in the given number of replicates (number_replicates_reliable) in all/at least one comparison.">
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122 <option value="FALSE">At least one</option>
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123 <option value="TRUE">All</option>
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124 </param>
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125 <!-- TODO which variances? -->
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126 <param argument="var.equal" name="var_equal" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Treat variances as equal" help="for t-test"/>
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127 <param argument="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use paired t-test" help=""/>
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128 <param argument="alternative" type="select" label="Alternative hypothesis" help="">
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129 <option value="two.sided">two.sided</option>
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130 <option value="greater">greater</option>
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131 <option value="less">less</option>
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132 </param>
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133 <param argument="pvalue_adjustment" type="select" label="Method for p-value adjustment" help="">
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134 <option value="holm">Holm</option>
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135 <option value="hochberg">Hochberg</option>
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136 <option value="hommel">Hommel</option>
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137 <option value="bonferroni">Bonferroni</option>
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138 <option value="BY">Benjamini &amp; Yekutieli (BY)</option>
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139 <option value="fdr" selected="true">Benjamini &amp; Hochberg (BH/fdr)</option>
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140 <option value="none">None</option>
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141 </param>
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142 <param argument="pvalue_decision" type="select" label="Choose whether to extract and visualize data based on adjusted p-values or raw p-values" help="">
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143 <option value="pvalueadj" selected="true">adjusted p-values</option>
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144 <option value="pvalue">raw p-values</option>
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145 </param>
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146 <param argument="significance_cutoff" type="float" value="0.05" min="0" max="1" label="Significance cutoff" help="All candidates with lower value are considered significantly affected"/>
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147 <param argument="color_up" type="color" value="#DC0000" label="Color for up-regulated candidates"/>
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148 <param argument="color_down" type="color" value="#3C5488" label="Color for down-regulated candidates"/>
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149 <param argument="color_none" type="color" value="#000000" label="Color for not significantly altered candidates"/>
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150 </xml>
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151
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152 <xml name="sample_genes_mapping">
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153 <param argument="sampleGenes" type="data" format="csv,tabular" optional="true" label="Accession - Gene name mapping" help="An optional table conatining columns Accession and Gene"/>
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154 <param argument="sampleMapping" type="data" format="csv,tabular" optional="true" label="Sample mapping" help="An optional table that is used to relate different conditions to ggplot facets. See help."/>
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155 </xml>
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156
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157 <xml name="citations">
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158 <citations>
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159 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
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160 author = "Isabel Karkossa",
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161 title = "proteomicsr",
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162 publisher = {UFZ GitLab},
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163 journal = {Git repository},
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164 year = "2023"
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165 note = "https://git.ufz.de/kratochv/proteomicsr"
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166 }
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167 </citation>
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168 </citations>
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169 </xml>
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170 <!-- TODO citations: helmholz codebase / doi -->
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171
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172
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173
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174 </macros>