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comparison dimet_enrichment_plot.xml @ 0:254408bfc5c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
author iuc
date Tue, 10 Oct 2023 11:57:25 +0000
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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>