Mercurial > repos > iuc > dimet_abundance_plot
comparison dimet_abundance_plot.xml @ 0:c9040bdb918c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
author | iuc |
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date | Tue, 10 Oct 2023 11:55:25 +0000 |
parents | |
children | 07164270ec13 |
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1 <tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> | |
2 <description> | |
3 Figures of metabolites total abundance as barplots (by DIMet) | |
4 </description> | |
5 <macros> | |
6 <token name="@TOOL_LABEL@">abundance plot</token> | |
7 <token name="@EXECUTABLE@">abundance_plot</token> | |
8 <import>macros.xml</import> | |
9 </macros> | |
10 <expand macro="requirements"/> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 @INIT_CONFIG@ | |
13 @INIT_ABUNDANCE_PLOT@ | |
14 @INIT_CONDITIONS@ | |
15 @INIT_TIMEPOINTS@ | |
16 @INIT_ENRICHMENT_METABOLITES@ | |
17 HYDRA_FULL_ERROR=1 python -m dimet | |
18 -cp '$__new_file_path__/config' | |
19 '++hydra.run.dir=abundance_plot' | |
20 '++figure_path=figures' | |
21 '++table_path=tables' | |
22 '++analysis={ | |
23 metabolites:${metabolites}, | |
24 dataset:{ | |
25 _target_:dimet.data.DatasetConfig, | |
26 name: "Galaxy DIMet run" | |
27 }, | |
28 method:{ | |
29 _target_: dimet.method.AbundancePlotConfig, | |
30 label: abundance_plot, | |
31 name: "Generate abundance plots", | |
32 barcolor: timepoint, | |
33 axisx: condition, | |
34 axisx_labeltilt: '${output_options.axisx_labeltilt}', | |
35 height_each_subfig: '${output_options.height_each_subfig}', | |
36 palette:${output_options.palette}, | |
37 as_grid:${output_options.as_grid}, | |
38 do_stripplot:${output_options.do_stripplot}, | |
39 figure_format:${output_options.figure_format} | |
40 }, | |
41 label: abundance_plot, | |
42 width_each_subfig: '${output_options.width_each_subfig}' | |
43 }' | |
44 '++analysis.dataset.label=' | |
45 '++analysis.timepoints=${timepoints}' | |
46 '++analysis.dataset.subfolder=' | |
47 '++analysis.dataset.conditions=${conds}' | |
48 #if $metadata_path: | |
49 '++analysis.dataset.metadata=metadata' | |
50 #end if | |
51 #if $abundance_file: | |
52 '++analysis.dataset.abundances=abundance' | |
53 #end if | |
54 @REMOVE_CONFIG@ | |
55 ]]></command> | |
56 <inputs> | |
57 <expand macro="input_parameters_abundance"/>xz | |
58 <expand macro="conditions"/> | |
59 <expand macro="timepoint"/> | |
60 <expand macro="compartments_abundance"/> | |
61 <expand macro="abundance_metabolites_list"/> | |
62 <section name="output_options" title="Output options"> | |
63 <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot" help="Please enter at max 1 statistical test by file"> | |
64 <option value="pastel">pastel</option> | |
65 <option value="Set1">Set1</option> | |
66 <option value="Set2">Set2</option> | |
67 <option value="Set3">Set3</option> | |
68 <option value="Dark2">Dark2</option> | |
69 </param> | |
70 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format"> | |
71 <option value="pdf">Pdf</option> | |
72 <option value="svg">Svg</option> | |
73 </param> | |
74 <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt" | |
75 help="Default value is 70."/> | |
76 <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots" | |
77 help="Default value is 3."/> | |
78 <param name="height_each_subfig" type="float" min="1.0" max="15.0" value="5.5" label="height of subfig plots" | |
79 help="Default value is 5.5"/> | |
80 <param name="as_grid" type="boolean" value="false" label="plot as grid" | |
81 help="Default value is false."/> | |
82 <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar" | |
83 help="Default value is false."/> | |
84 | |
85 </section> | |
86 </inputs> | |
87 <outputs> | |
88 <collection name="report" type="list"> | |
89 <discover_datasets pattern="__designation_and_ext__" directory="figures"/> | |
90 </collection> | |
91 </outputs> | |
92 <tests> | |
93 <test> | |
94 <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/> | |
95 <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/> | |
96 <param name="conditions" value='sgLDHA'/> | |
97 <param name="timepoint" value='T0,T24'/> | |
98 <param name="compartments" value='endo'/> | |
99 <param name="metabolites_list" value="Fru1P"/> | |
100 <section name="output_options"> | |
101 <param name="axisx_labeltilt" value="70"/> | |
102 <param name="palette" value="pastel"/> | |
103 <param name="width_each_subfig" value="3.0"/> | |
104 <param name="height_each_subfig" value="5.5"/> | |
105 <param name="as_grid" value="false"/> | |
106 <param name="do_stripplot" value="false"/> | |
107 <param name="figure_format" value="svg"/> | |
108 </section> | |
109 <output_collection name="report" type="list" count="2"> | |
110 <element file="bars_endo_Fru1P-total_abundance.svg" name="bars_endo_Fru1P-total_abundance" ftype="svg" compare="sim_size" delta="100"/> | |
111 <element file="legend.svg" name="legend" ftype="svg" compare="sim_size" delta="100"/> | |
112 </output_collection> | |
113 </test> | |
114 </tests> | |
115 <help><![CDATA[ | |
116 | |
117 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/). | |
118 | |
119 DIMet total abundances plot performs comparative bars for visualization of the total abundances of each metabolite across the different conditions present in your data and all/selected time points. All (or selected) metabolites are processed automatically. | |
120 | |
121 The figures in .pdf format are of publication quality, and as they are vectorial images you can open them and customize aesthetics with a professional image software such as Inkscape, Adobe Illustrator, Sketch, CorelDRAW, etc. | |
122 | |
123 | |
124 **Input data files** | |
125 | |
126 For running DIMet @EXECUTABLE@ you need the following .csv files : | |
127 | |
128 - The total **abundances** file, and | |
129 | |
130 - The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**). | |
131 | |
132 | |
133 The total abundances file must be organized as a matrix: | |
134 - The first column must contain Metabolite IDs that are unique (not repeated) within the file. | |
135 - The rest of the columns correspond to the samples | |
136 - The rows correspond to the metabolites | |
137 - The values must be tab separated, with the first row containing the sample/column labels. | |
138 | |
139 | |
140 | |
141 Example - Metabolites **abundances**: | |
142 | |
143 =============== ================== ================== ================== ================== ================== ================== | |
144 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** | |
145 =============== ================== ================== ================== ================== ================== ================== | |
146 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956 | |
147 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051 | |
148 Glc6P 2310 2142 2683 1683 012532068 1252172 | |
149 Gly3P 399298 991656565 525195 6365231 89451625 4952651963 | |
150 IsoCit 0 0 0 84915613 856236 954651610 | |
151 =============== ================== ================== ================== ================== ================== ================== | |
152 | |
153 | |
154 **Metadata File Information** | |
155 | |
156 Provide a tab-separated file that has the names of the samples in the first column and one header row. | |
157 Column names must be exactly in this order: | |
158 | |
159 name_to_plot | |
160 condition | |
161 timepoint | |
162 timenum | |
163 compartment | |
164 original_name | |
165 | |
166 | |
167 Example **Metadata File**: | |
168 | |
169 | |
170 ==================== =============== ============= ============ ================ ================= | |
171 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name** | |
172 -------------------- --------------- ------------- ------------ ---------------- ----------------- | |
173 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01 | |
174 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02 | |
175 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03 | |
176 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04 | |
177 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05 | |
178 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06 | |
179 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07 | |
180 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08 | |
181 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01 | |
182 Control_med_T24-1 Control T24 24 med MCF001090_TD02 | |
183 Control_med_T24-2 Control T24 24 med MCF001090_TD03 | |
184 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04 | |
185 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05 | |
186 Control_med_T0-1 Control T0 0 med MCF001090_TD06 | |
187 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07 | |
188 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08 | |
189 ==================== =============== ============= ============ ================ ================= | |
190 | |
191 | |
192 The column **original_name** must have the names of the samples as given in your data. | |
193 | |
194 The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that | |
195 are meaningful is a better choice, as we will take them to display the results. | |
196 | |
197 The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc) | |
198 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!). | |
199 | |
200 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the | |
201 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. | |
202 | |
203 | |
204 **Running the analysis** | |
205 | |
206 | |
207 You can precise how you want your analysis to be executed, with the parameters: | |
208 | |
209 - **conditions** : the conditions present in your data, exactly in the ORDER you want them to appear both in the x axis and in the legend. | |
210 | |
211 - **timepoints** : the selected (you can select all) time points, that will be shown in the x axis. | |
212 | |
213 - **width_each_subfig** : the desired width (in inches) for the the individual metabolites' figures | |
214 | |
215 | |
216 | |
217 There exist hints on use that will guide you, next to the parameters. | |
218 | |
219 | |
220 The output consists of bar-plot figures, one by each metabolite, and one legend .pdf file, common to all the produced figures. | |
221 | |
222 | |
223 | |
224 **Available data for testing** | |
225 | |
226 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent | |
227 files for you are located in the subfolders inside the data folder). | |
228 Tou can also use the minimal data examples from https://zenodo.org/record/8380706 | |
229 | |
230 ]]> | |
231 </help> | |
232 <expand macro="citations"/> | |
233 </tool> |