Mercurial > repos > mbernt > proteomicsr_intensity_workflow

comparison macros.xml @ 0:31212f7e7611 draft default tip

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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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-1:000000000000 0:31212f7e7611
1 <macros>
2 <token name="@TOOL_VERSION@">0.1.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">r-proteomicsr</requirement>
7 <!-- <requirement type="package" version="2.58.0">bioconductor-biomart</requirement>
8 <requirement type="package" version="4.10.0">bioconductor-clusterprofiler</requirement>
9 <requirement type="package" version="1.24.0">bioconductor-dep</requirement>
10 <requirement type="package" version="2.18.0">bioconductor-complexheatmap</requirement>
11 <requirement type="package" version="1.20.0">bioconductor-kinswingr</requirement>
12 <requirement type="package" version="0.4.15">r-circlize</requirement>
13 <requirement type="package" version="3.4.0">r-classdiscovery</requirement>
14 <requirement type="package" version="0.92">r-corrplot</requirement>
15 <requirement type="package" version="0.3.4">r-dendsort</requirement>
16 <requirement type="package" version="1.63_1">r-dynamictreecut</requirement>
17 <requirement type="package" version="3.4.2">r-ggplot2</requirement>
18 <requirement type="package" version="0.6.0">r-ggpubr</requirement>
19 <requirement type="package" version="6.3.2">r-mixomics</requirement>
20 <requirement type="package" version="7.5.1">r-msigdbr</requirement>
21 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
22 <requirement type="package" version="1.8.9">r-plyr</requirement>
23 <requirement type="package" version="2.1.4">r-readr</requirement>
24 <requirement type="package" version="1.4.4">r-reshape2</requirement>
25 <requirement type="package" version="1.2.1">r-scales</requirement>
26 <requirement type="package" version="1.4.8">r-splitstackshape</requirement>
27 <requirement type="package" version="1.3.0">r-tidyr</requirement>
28 <requirement type="package" version="1.71">r-wgcna</requirement>
29 <requirement type="package" version="2.3.4">r-dbplyr</requirement> -->
30
31 <!-- conda create -y \-\-quiet \-\-strict-channel-priority \-\-solver libmamba \-\-override-channels \-\-channel conda-forge \-\-channel bioconda \-\-channel defaults \-\-name
32 __r-proteomicsr@0.1.0
33 "bioconductor-biomart=2.58.0" # needed update https://github.com/grimbough/biomaRt/issues/87
34 "bioconductor-clusterprofiler=4.10.0" #(newer needed, otherwise conflict with bioconductor-biomart)
35 "bioconductor-dep=1.24.0" # same
36 bioconductor-complexheatmap=2.18.0
37 bioconductor-kinswingr
38 r-circlize=0.4.15
39 r-classdiscovery=3.4.0
40 r-corrplot=0.92 r-dendsort=0.3.4
41 r-dynamictreecut=1.63_1
42 r-ggplot2=3.4.2
43 r-ggpubr=0.6.0
44 r-mixomics=6.3.2
45 r-msigdbr=7.5.1
46 r-pheatmap=1.0.12
47 r-plyr=1.8.9
48 r-readr=2.1.4
49 r-reshape2=1.4.4
50 r-scales=1.2.1
51 r-splitstackshape=1.4.8
52 r-tidyr=1.3.0
53 r-wgcna=1.71
54 "r-dbplyr<2.4"
55 -->
56 <!-- <requirement type="package" version="3.0.0">r-ggsci</requirement> -->
57 <!-- <requirement type="package" version="2.3">r-gridextra</requirement> -->
58
59 <yield/>
60 </requirements>
61 </xml>
62
63 <token name="@READ_INPUTS@"><![CDATA[
64 #if $sampleTable.ext == 'csv'
65 sampleTable <- read.csv("$sampleTable", row.names = 1)
66 #else
67 sampleTable <- read.delim("$sampleTable", header = TRUE, row.names = 1, sep = "\t")
68 #end if
69 @READ_SAMPLE_GENES_MAPPING@
70 ]]></token>
71
72 <token name="@READ_SAMPLE_GENES_MAPPING@"><![CDATA[
73 #if $sampleGenes
74 #if $sampleGenes.ext == 'csv'
75 sampleGenes <- read.csv("$sampleGenes", row.names = 1)
76 #else
77 sampleGenes <- read.delim("$sampleGenes", header = TRUE, row.names = 1, sep = "\t")
78 #end if
79 #else
80 sampleGenes <- NULL
81 #end if
82 #if $sampleMapping
83 #if $sampleMapping.ext == 'csv'
84 sampleMapping <- read.csv("$sampleMapping", row.names = 1)
85 #else
86 sampleMapping <- read.delim("$sampleMapping", header = TRUE, row.names = 1, sep = "\t")
87 #end if
88 #else
89 sampleMapping <- NULL
90 #end if
91 ]]></token>
92
93 <token name="@COMMON_WF_PARAMETERS@"><![CDATA[
94 sampleTable,
95 sampleGenes = sampleGenes, ## this implies more output data sets!
96 sampleMapping = sampleMapping,
97 remove_outliers = $remove_outliers,
98 median_normalize = $median_normalize,
99 number_replicates_reliable = $number_replicates_reliable,
100 reliable_all_comparisons = $reliable_all_comparisons,
101 alternative = "$alternative",
102 var.equal = $var_equal,
103 paired = $paired,
104 pvalue_decision = "$pvalue_decision",
105 pvalue_adjustment = "$pvalue_adjustment",
106 significance_cutoff = $significance_cutoff,
107 color_up = "${color_up}FF",
108 color_none = "${color_none}FF",
109 color_down = "${color_down}FF"
110 ]]></token>
111 <xml name="common_wf_paramerters">
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."/>
113 <expand macro="sample_genes_mapping"/>
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"/>
115 <param argument="median_normalize" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Apply median normalization" help=""/>
116
117 <yield/>
118
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)"/>
120 <!--TODO formulation unclear, comparisons between what? Samples? -->
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.">
122 <option value="FALSE">At least one</option>
123 <option value="TRUE">All</option>
124 </param>
125 <!-- TODO which variances? -->
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"/>
127 <param argument="paired" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use paired t-test" help=""/>
128 <param argument="alternative" type="select" label="Alternative hypothesis" help="">
129 <option value="two.sided">two.sided</option>
130 <option value="greater">greater</option>
131 <option value="less">less</option>
132 </param>
133 <param argument="pvalue_adjustment" type="select" label="Method for p-value adjustment" help="">
134 <option value="holm">Holm</option>
135 <option value="hochberg">Hochberg</option>
136 <option value="hommel">Hommel</option>
137 <option value="bonferroni">Bonferroni</option>
138 <option value="BY">Benjamini &amp; Yekutieli (BY)</option>
139 <option value="fdr" selected="true">Benjamini &amp; Hochberg (BH/fdr)</option>
140 <option value="none">None</option>
141 </param>
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="">
143 <option value="pvalueadj" selected="true">adjusted p-values</option>
144 <option value="pvalue">raw p-values</option>
145 </param>
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"/>
147 <param argument="color_up" type="color" value="#DC0000" label="Color for up-regulated candidates"/>
148 <param argument="color_down" type="color" value="#3C5488" label="Color for down-regulated candidates"/>
149 <param argument="color_none" type="color" value="#000000" label="Color for not significantly altered candidates"/>
150 </xml>
151
152 <xml name="sample_genes_mapping">
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"/>
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."/>
155 </xml>
156
157 <xml name="citations">
158 <citations>
159 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
160 author = "Isabel Karkossa",
161 title = "proteomicsr",
162 publisher = {UFZ GitLab},
163 journal = {Git repository},
164 year = "2023"
165 note = "https://git.ufz.de/kratochv/proteomicsr"
166 }
167 </citation>
168 </citations>
169 </xml>
170 <!-- TODO citations: helmholz codebase / doi -->
171
172
173
174 </macros>