Mercurial > repos > iuc > dimet_enrichment_plot
comparison dimet_enrichment_plot.xml @ 0:254408bfc5c0 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 11:57:25 +0000 |
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children | 79720105f8c0 |
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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 mean enrichment by metabolite, as line-plots (by DIMet) | |
4 </description> | |
5 <macros> | |
6 <token name="@TOOL_LABEL@">enrichment plot</token> | |
7 <token name="@EXECUTABLE@">enrichment_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_ENRICHMENT_PLOT@ | |
14 @INIT_CONDITIONS@ | |
15 @INIT_TIMEPOINTS@ | |
16 @INIT_ENRICHMENT_METABOLITES@ | |
17 HYDRA_FULL_ERROR=1 python -m dimet | |
18 -cp '$__new_file_path__/config' | |
19 '++hydra.run.dir=mean_enrichment_line_plot' | |
20 '++figure_path=figures' | |
21 '++table_path=tables' | |
22 '++analysis={ | |
23 metabolites:${metabolites}, | |
24 dataset:{ | |
25 _target_:dimet.data.DatasetConfig, | |
26 name: "Galaxy DIMet run" | |
27 }, | |
28 method:{ | |
29 _target_: dimet.method.MeanEnrichmentLinePlotConfig, | |
30 label: mean_enrichment_line_plot, | |
31 name: "Generate mean enrichment line plots", | |
32 color_lines_by: condition, | |
33 palette_condition: muted, | |
34 palette_metabolite: auto_multi_color, | |
35 xaxis_title: ${output_options.xaxis_title}, | |
36 alpha: ${output_options.alpha}, | |
37 plot_grouped_by_dict: null, | |
38 ###width_subplot: '${output_options.width_subplot}', | |
39 height_subplot: ${output_options.height_subplot}, | |
40 figure_format:${output_options.figure_format}, | |
41 as_grid:${output_options.as_grid} | |
42 }, | |
43 width_subplot: '${output_options.width_subplot}', | |
44 label: enrich_lineplot | |
45 }' | |
46 '++analysis.dataset.label=' | |
47 '++analysis.timepoints=${timepoints}' | |
48 '++analysis.dataset.subfolder=' | |
49 '++analysis.dataset.conditions=${conds}' | |
50 | |
51 #if $metadata_path: | |
52 '++analysis.dataset.metadata=metadata' | |
53 #end if | |
54 #if $me_or_frac_contrib_file: | |
55 '++analysis.dataset.mean_enrichment=me_or_frac_contrib' | |
56 #end if | |
57 @REMOVE_CONFIG@ | |
58 ]]></command> | |
59 <inputs> | |
60 <expand macro="input_parameters_enrichment"/> | |
61 <expand macro="conditions"/> | |
62 <expand macro="timepoint"/> | |
63 <expand macro="compartments_enrichment"/> | |
64 <expand macro="enrichment_metabolites_list"/> | |
65 <section name="output_options" title="Output options"> | |
66 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format"> | |
67 <option value="pdf">Pdf</option> | |
68 <option value="svg">Svg</option> | |
69 </param> | |
70 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots" | |
71 help="Default value is 1."/> | |
72 <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots" | |
73 help="Default value is 3."/> | |
74 <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots" | |
75 help="Default value is 3."/> | |
76 <param name="as_grid" type="boolean" value="false" label="plot as grid" | |
77 help="Default value is false."/> | |
78 <param name="xaxis_title" type="text" value="Time" optional="false" label="xaxis_title to add to output files" > | |
79 <sanitizer invalid_char=""> | |
80 <valid initial="string.ascii_letters,string.digits"> | |
81 <add value="_" /> | |
82 </valid> | |
83 </sanitizer> | |
84 </param> | |
85 </section> | |
86 </inputs> | |
87 | |
88 <outputs> | |
89 <collection name="report" type="list"> | |
90 <discover_datasets pattern="__designation_and_ext__" directory="figures"/> | |
91 </collection> | |
92 </outputs> | |
93 <tests> | |
94 <test> | |
95 <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/> | |
96 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> | |
97 <param name="conditions" value='Control,L-Cycloserine'/> | |
98 <param name="timepoint" value='T0,T2h'/> | |
99 <param name="compartments" value='cell,med'/> | |
100 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/> | |
101 <section name="output_options"> | |
102 <param name="alpha" value="1.0"/> | |
103 <param name="height_subplot" value="6.4"/> | |
104 <param name="width_subplot" value="4.0"/> | |
105 <param name="xaxis_title" value="Time"/> | |
106 <param name="figure_format" value="svg"/> | |
107 </section> | |
108 | |
109 <output_collection name="report" type="list" count="6"> | |
110 <element file="mean_enrichment-cell-Fumaric_acid.svg" name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/> | |
111 <element file="mean_enrichment-cell-Glycine.svg" name="mean_enrichment-cell-Glycine" ftype="svg" compare="sim_size" delta="100"/> | |
112 <element file="mean_enrichment-cell-L-Proline.svg" name="mean_enrichment-cell-L-Proline" ftype="svg" compare="sim_size" delta="100"/> | |
113 <element file="mean_enrichment-med-Fumaric_acid.svg" name="mean_enrichment-med-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/> | |
114 <element file="mean_enrichment-med-Glycine.svg" name="mean_enrichment-med-Glycine" ftype="svg" compare="sim_size" delta="100"/> | |
115 <element file="mean_enrichment-med-L-Proline.svg" name="mean_enrichment-med-L-Proline" ftype="svg" compare="sim_size" delta="100"/> | |
116 </output_collection> | |
117 </test> | |
118 </tests> | |
119 <help><![CDATA[ | |
120 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/). | |
121 | |
122 DIMet enrichment plot performs line-plot figures for visualization of the (stable isotope) mean enrichment across all the time points present in your data, for each metabolite. All (or selected) metabolites are processed automatically. | |
123 | |
124 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. | |
125 | |
126 | |
127 **Input data files** | |
128 | |
129 For running DIMet @EXECUTABLE@ you need the following .csv files : | |
130 | |
131 - The mean **enrichment** file, and | |
132 | |
133 - The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**). | |
134 | |
135 | |
136 The mean enrichment file must be organized as a matrix: | |
137 | |
138 - The first column must contain Metabolite IDs that are unique (not repeated) within the file. | |
139 | |
140 - The rest of the columns correspond to the samples | |
141 | |
142 - The rows correspond to the metabolites | |
143 | |
144 - The values must be tab separated, with the first row containing the sample/column labels. | |
145 | |
146 | |
147 Example - mean **enrichment** or labeled fractional contributions: | |
148 | |
149 =============== ================== ================== ================== ================== ================== ================== | |
150 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** | |
151 =============== ================== ================== ================== ================== ================== ================== | |
152 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9 | |
153 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68 | |
154 Glc6P 0.06 0.66 2683 0.06 2068 2172 | |
155 Gly3P 0.06 0.06 0.06 1 5 3 | |
156 IsoCit 0.06 1 0.49 0.36 6 10 | |
157 =============== ================== ================== ================== ================== ================== ================== | |
158 | |
159 | |
160 | |
161 **Metadata File Information** | |
162 | |
163 Provide a tab-separated file that has the names of the samples in the first column and one header row. | |
164 Column names must be exactly in this order: | |
165 | |
166 name_to_plot | |
167 condition | |
168 timepoint | |
169 timenum | |
170 compartment | |
171 original_name | |
172 | |
173 | |
174 Example **Metadata File**: | |
175 | |
176 | |
177 ==================== =============== ============= ============ ================ ================= | |
178 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name** | |
179 -------------------- --------------- ------------- ------------ ---------------- ----------------- | |
180 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01 | |
181 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02 | |
182 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03 | |
183 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04 | |
184 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05 | |
185 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06 | |
186 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07 | |
187 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08 | |
188 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01 | |
189 Control_med_T24-1 Control T24 24 med MCF001090_TD02 | |
190 Control_med_T24-2 Control T24 24 med MCF001090_TD03 | |
191 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04 | |
192 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05 | |
193 Control_med_T0-1 Control T0 0 med MCF001090_TD06 | |
194 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07 | |
195 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08 | |
196 ==================== =============== ============= ============ ================ ================= | |
197 | |
198 | |
199 The column **original_name** must have the names of the samples as given in your data. | |
200 | |
201 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 | |
202 are meaningful is a better choice, as we will take them to display the results. | |
203 | |
204 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) | |
205 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!). | |
206 | |
207 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the | |
208 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. | |
209 | |
210 | |
211 **Running the analysis** | |
212 | |
213 | |
214 You can precise how you want your analysis to be executed, with the parameters: | |
215 | |
216 - **conditions**: the conditions present in your data, exactly in the ORDER you want them to appear in the legend of each figure. | |
217 | |
218 - **width_subplot** : the desired width (in inches) for the the individual metabolites' figures | |
219 | |
220 There exist hints on use that will guide you, next to the parameters. | |
221 | |
222 Note that this plot makes sense when you dispose of two or more time-points. If your setup is not a time-series, you may rather use our metabologram integration with the differential mean enrichment (comparing the conditions of your choice). | |
223 | |
224 The output consists of line-plot figures, one by each metabolite. | |
225 | |
226 **Available data for testing** | |
227 | |
228 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent | |
229 files for you are located in the subfolders inside the data folder). | |
230 Tou can also use the minimal data examples from https://zenodo.org/record/8380706 | |
231 | |
232 ]]> | |
233 </help> | |
234 <expand macro="citations"/> | |
235 </tool> |