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comparison dimet_enrichment_plot.xml @ 0:1bfe9f9608e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
author iuc
date Fri, 21 Jun 2024 18:45:22 +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_PLOT_CONDITIONS@
15 @INIT_TIMEPOINTS@
16 @INIT_ENRICHMENT_METABOLITES@
17 HYDRA_FULL_ERROR=1 python -m dimet
18 '++hydra.run.dir=.'
19 '++figure_path=figures'
20 '++table_path=tables'
21 '++analysis={
22 metabolites:${metabolites},
23 dataset:{
24 _target_:dimet.data.DatasetConfig,
25 name: "Galaxy DIMet run"
26 },
27 method:{
28 _target_: dimet.method.MeanEnrichmentLinePlotConfig,
29 label: mean_enrichment_line_plot,
30 name: "Generate mean enrichment line plots",
31 palette_condition: ${output_options.palette},
32 palette_metabolite: auto_multi_color,
33 xaxis_title: ${output_options.xaxis_title},
34 alpha: ${output_options.alpha},
35 plot_grouped_by_dict: null,
36 color_lines_by: '${output_options.color_lines_by}',
37 height_subplot: ${output_options.height_subplot},
38 figure_format:${output_options.figure_format},
39 as_grid:${output_options.as_grid}
40 },
41 width_subplot: '${output_options.width_subplot}',
42 label: enrich_lineplot
43 }'
44 '++analysis.dataset.label='
45 '++analysis.timepoints=${timepoints}'
46 '++analysis.dataset.subfolder='
47 '++analysis.dataset.conditions=${conditions}'
48
49 #if $metadata_path:
50 '++analysis.dataset.metadata=metadata'
51 #end if
52 #if $me_or_frac_contrib_file:
53 '++analysis.dataset.mean_enrichment=me_or_frac_contrib'
54 #end if
55 @REMOVE_CONFIG@
56 ]]></command>
57 <inputs>
58 <expand macro="input_parameters_enrichment"/>
59 <expand macro="plot_factor_list"/>
60 <expand macro="timepoint"/>
61 <expand macro="compartments_enrichment"/>
62 <expand macro="enrichment_metabolites_list"/>
63 <section name="output_options" title="Output options">
64 <param name="figure_format" type="select" value="pdf" display="radio" label="Select output figure format" help="Please enter at max 1 format">
65 <option value="pdf">Pdf</option>
66 <option value="svg">Svg</option>
67 </param>
68 <expand macro="palette"/>
69 <param name="color_lines_by" type="select" value="condition" display="radio" label="Select color for lines" help="Please enter at max 1 format">
70 <option value="condition">Condition</option>
71 <option value="metabolite">Metabolite</option>
72 </param>
73 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
74 help="Default value is 1."/>
75 <param name="height_subplot" type="float" min="1.0" max="15.0" value="6.4" label="height of subfig plots"
76 help="Default value is 3."/>
77 <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots"
78 help="Default value is 3."/>
79 <param name="as_grid" type="boolean" value="false" label="plot as grid"
80 help="Default value is false."/>
81 <param name="xaxis_title" type="text" value="Time" optional="false" label="xaxis_title to add to output files" >
82 <sanitizer invalid_char="">
83 <valid initial="string.ascii_letters,string.digits">
84 <add value="_" />
85 </valid>
86 </sanitizer>
87 </param>
88 </section>
89 </inputs>
90
91 <outputs>
92 <collection name="report" type="list">
93 <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
94 </collection>
95 </outputs>
96 <tests>
97 <test>
98 <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/>
99 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
100 <repeat name="plot_factor_list">
101 <param name="condition" value="Control"/>
102 </repeat>
103 <repeat name="plot_factor_list">
104 <param name="condition" value="L-Cycloserine"/>
105 </repeat>
106 <param name="timepoint" value='T0,T2h'/>
107 <param name="compartments" value='cell,med'/>
108 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
109 <section name="output_options">
110 <param name="alpha" value="1.0"/>
111 <param name="height_subplot" value="6.4"/>
112 <param name="width_subplot" value="4.0"/>
113 <param name="xaxis_title" value="Time"/>
114 <param name="color_lines_by" value="condition"/>
115 <param name="figure_format" value="svg"/>
116 </section>
117
118 <output_collection name="report" type="list" count="6">
119 <element file="mean_enrichment-cell-Fumaric_acid.svg" name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
120 <element file="mean_enrichment-cell-Glycine.svg" name="mean_enrichment-cell-Glycine" ftype="svg" compare="sim_size" delta="100"/>
121 <element file="mean_enrichment-cell-L-Proline.svg" name="mean_enrichment-cell-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
122 <element file="mean_enrichment-med-Fumaric_acid.svg" name="mean_enrichment-med-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/>
123 <element file="mean_enrichment-med-Glycine.svg" name="mean_enrichment-med-Glycine" ftype="svg" compare="sim_size" delta="100"/>
124 <element file="mean_enrichment-med-L-Proline.svg" name="mean_enrichment-med-L-Proline" ftype="svg" compare="sim_size" delta="100"/>
125 </output_collection>
126 </test>
127 </tests>
128 <help><![CDATA[
129 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
130
131 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.
132
133 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.
134
135
136 **Input data files**
137
138 For running DIMet @EXECUTABLE@ you need the following .csv files :
139
140 - The mean **enrichment** file, and
141
142 - The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**).
143
144
145 The mean enrichment file must be organized as a matrix:
146
147 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
148
149 - The rest of the columns correspond to the samples
150
151 - The rows correspond to the metabolites
152
153 - The values must be tab separated, with the first row containing the sample/column labels.
154
155
156 Example - mean **enrichment** or labeled fractional contributions:
157
158 =============== ================== ================== ================== ================== ================== ==================
159 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
160 =============== ================== ================== ================== ================== ================== ==================
161 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9
162 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68
163 Glc6P 0.06 0.66 2683 0.06 2068 2172
164 Gly3P 0.06 0.06 0.06 1 5 3
165 IsoCit 0.06 1 0.49 0.36 6 10
166 =============== ================== ================== ================== ================== ================== ==================
167
168
169
170 **Metadata File Information**
171
172 Provide a tab-separated file that has the names of the samples in the first column and one header row.
173 Column names must be exactly in this order:
174
175 name_to_plot
176 condition
177 timepoint
178 timenum
179 compartment
180 original_name
181
182
183 Example **Metadata File**:
184
185
186 ==================== =============== ============= ============ ================ =================
187 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
188 -------------------- --------------- ------------- ------------ ---------------- -----------------
189 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
190 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
191 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
192 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
193 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
194 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
195 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
196 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
197 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
198 Control_med_T24-1 Control T24 24 med MCF001090_TD02
199 Control_med_T24-2 Control T24 24 med MCF001090_TD03
200 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
201 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
202 Control_med_T0-1 Control T0 0 med MCF001090_TD06
203 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
204 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
205 ==================== =============== ============= ============ ================ =================
206
207
208 The column **original_name** must have the names of the samples as given in your data.
209
210 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
211 are meaningful is a better choice, as we will take them to display the results.
212
213 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)
214 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
215
216 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
217 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
218
219
220 **Running the analysis**
221
222
223 You can precise how you want your analysis to be executed, with the parameters:
224
225 - **conditions**: the conditions present in your data, exactly in the ORDER you want them to appear in the legend of each figure.
226
227 - **width_subplot** : the desired width (in inches) for the the individual metabolites' figures
228
229 There exist hints on use that will guide you, next to the parameters.
230
231 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).
232
233 The output consists of line-plot figures, one by each metabolite.
234
235 **Available data for testing**
236
237 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
238 files for you are located in the subfolders inside the data folder).
239 You can also use the minimal data examples from https://zenodo.org/record/10579891
240
241 ]]>
242 </help>
243 <expand macro="citations"/>
244 </tool>