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comparison dimet_abundance_plot.xml @ 0:4098d42e27f7 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 18:46:51 +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 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_ABUNDANCE_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:${metabolites},
23 dataset:{
24 _target_:dimet.data.DatasetConfig,
25 name: "Galaxy DIMet run"
26 },
27 method:{
28 _target_: dimet.method.AbundancePlotConfig,
29 label: abundance_plot,
30 name: "Generate abundance plots",
31 barcolor: '${output_options.bar_color}',
32 axisx: ${axisx},
33 axisx_labeltilt: '${output_options.axisx_labeltilt}',
34 height_each_subfig: '${output_options.height_each_subfig}',
35 palette:${output_options.palette},
36 as_grid:${output_options.as_grid},
37 x_text_modify_as:null,
38 do_stripplot:${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=${timepoints}'
46 '++analysis.dataset.subfolder='
47 '++analysis.dataset.conditions=${conditions}'
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"/>
58 <expand macro="plot_abundance_factor_list"/>
59 <expand macro="timepoint"/>
60 <expand macro="compartments_abundance"/>
61 <expand macro="abundance_metabolites_list"/>
62 <section name="output_options" title="Output options">
63 <expand macro="palette"/>
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 <param name="bar_color" type="select" value="timepoint" display="radio" label="Select output figure barcolor" help="Please enter at max 1 format">
69 <option value="timepoint">timepoint</option>
70 <option value="condition">condition</option>
71 </param>
72 <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt"
73 help="Default value is 70."/>
74 <param name="width_each_subfig" type="float" min="1.0" max="15.0" value="3.0" label="width of subfig plots"
75 help="Default value is 3."/>
76 <param name="height_each_subfig" type="float" min="1.0" max="15.0" value="5.5" label="height of subfig plots"
77 help="Default value is 5.5"/>
78 <param name="as_grid" type="boolean" value="false" label="plot as grid"
79 help="Default value is false."/>
80 <param name="do_stripplot" type="boolean" value="false" label="add strip plot on abundance bar"
81 help="Default value is false."/>
82 </section>
83 </inputs>
84 <outputs>
85 <collection name="report" type="list">
86 <discover_datasets pattern="__designation_and_ext__" directory="figures"/>
87 </collection>
88 </outputs>
89 <tests>
90 <test>
91 <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/>
92 <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/>
93 <repeat name="plot_abundance_factor_list">
94 <param name="condition" value="sgLDHA"/>
95 </repeat>
96 <param name="timepoint" value='T0,T24'/>
97 <param name="compartments" value='endo'/>
98 <param name="metabolites_list" value="Fru1P"/>
99 <section name="output_options">
100 <param name="axisx_labeltilt" value="70"/>
101 <param name="bar_color" value="timepoint"/>
102 <param name="axisx" value="condition"/>
103 <param name="palette" value="pastel"/>
104 <param name="width_each_subfig" value="3.0"/>
105 <param name="height_each_subfig" value="5.5"/>
106 <param name="as_grid" value="false"/>
107 <param name="do_stripplot" value="false"/>
108 <param name="figure_format" value="svg"/>
109 </section>
110 <output_collection name="report" type="list" count="2">
111 <element file="bars_endo_Fru1P-total_abundance.svg" name="bars_endo_Fru1P-total_abundance" ftype="svg" compare="sim_size" delta="100"/>
112 <element file="legend.svg" name="legend" ftype="svg" compare="sim_size" delta="100"/>
113 </output_collection>
114 </test>
115 </tests>
116 <help><![CDATA[
117
118 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/).
119
120 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.
121
122 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.
123
124
125 **Input data files**
126
127 For running DIMet @EXECUTABLE@ you need the following .csv files :
128
129 - The total **abundances** file, and
130
131 - The metadata file, a unique file with the description of the samples. This file is compulsory (see section **Metadata File Information**).
132
133
134 The total abundances file must be organized as a matrix:
135 - The first column must contain Metabolite IDs that are unique (not repeated) within the file.
136 - The rest of the columns correspond to the samples
137 - The rows correspond to the metabolites
138 - The values must be tab separated, with the first row containing the sample/column labels.
139
140
141
142 Example - Metabolites **abundances**:
143
144 =============== ================== ================== ================== ================== ================== ==================
145 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06**
146 =============== ================== ================== ================== ================== ================== ==================
147 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956
148 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051
149 Glc6P 2310 2142 2683 1683 012532068 1252172
150 Gly3P 399298 991656565 525195 6365231 89451625 4952651963
151 IsoCit 0 0 0 84915613 856236 954651610
152 =============== ================== ================== ================== ================== ================== ==================
153
154
155 **Metadata File Information**
156
157 Provide a tab-separated file that has the names of the samples in the first column and one header row.
158 Column names must be exactly in this order:
159
160 name_to_plot
161 condition
162 timepoint
163 timenum
164 compartment
165 original_name
166
167
168 Example **Metadata File**:
169
170
171 ==================== =============== ============= ============ ================ =================
172 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name**
173 -------------------- --------------- ------------- ------------ ---------------- -----------------
174 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01
175 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02
176 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03
177 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04
178 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05
179 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06
180 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07
181 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08
182 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01
183 Control_med_T24-1 Control T24 24 med MCF001090_TD02
184 Control_med_T24-2 Control T24 24 med MCF001090_TD03
185 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04
186 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05
187 Control_med_T0-1 Control T0 0 med MCF001090_TD06
188 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07
189 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08
190 ==================== =============== ============= ============ ================ =================
191
192
193 The column **original_name** must have the names of the samples as given in your data.
194
195 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
196 are meaningful is a better choice, as we will take them to display the results.
197
198 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)
199 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).
200
201 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the
202 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column.
203
204
205 **Running the analysis**
206
207
208 You can precise how you want your analysis to be executed, with the parameters:
209
210 - **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.
211
212 - **timepoints** : the selected (you can select all) time points, that will be shown in the x axis.
213
214 - **width_each_subfig** : the desired width (in inches) for the the individual metabolites' figures
215
216
217
218 There exist hints on use that will guide you, next to the parameters.
219
220
221 The output consists of bar-plot figures, one by each metabolite, and one legend .pdf file, common to all the produced figures.
222
223
224
225 **Available data for testing**
226
227 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
228 files for you are located in the subfolders inside the data folder).
229 You can also use the minimal data examples from https://zenodo.org/record/10579891
230
231 ]]>
232 </help>
233 <expand macro="citations"/>
234 </tool>