Mercurial > repos > iuc > dimet_enrichment_plot
comparison dimet_enrichment_plot.xml @ 1:79720105f8c0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d
author | iuc |
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date | Tue, 23 Jan 2024 14:55:42 +0000 |
parents | 254408bfc5c0 |
children | 2de209fb390b |
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0:254408bfc5c0 | 1:79720105f8c0 |
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27 }, | 27 }, |
28 method:{ | 28 method:{ |
29 _target_: dimet.method.MeanEnrichmentLinePlotConfig, | 29 _target_: dimet.method.MeanEnrichmentLinePlotConfig, |
30 label: mean_enrichment_line_plot, | 30 label: mean_enrichment_line_plot, |
31 name: "Generate mean enrichment line plots", | 31 name: "Generate mean enrichment line plots", |
32 color_lines_by: condition, | |
33 palette_condition: muted, | 32 palette_condition: muted, |
34 palette_metabolite: auto_multi_color, | 33 palette_metabolite: auto_multi_color, |
35 xaxis_title: ${output_options.xaxis_title}, | 34 xaxis_title: ${output_options.xaxis_title}, |
36 alpha: ${output_options.alpha}, | 35 alpha: ${output_options.alpha}, |
37 plot_grouped_by_dict: null, | 36 plot_grouped_by_dict: null, |
38 ###width_subplot: '${output_options.width_subplot}', | 37 color_lines_by: '${output_options.color_lines_by}', |
39 height_subplot: ${output_options.height_subplot}, | 38 height_subplot: ${output_options.height_subplot}, |
40 figure_format:${output_options.figure_format}, | 39 figure_format:${output_options.figure_format}, |
41 as_grid:${output_options.as_grid} | 40 as_grid:${output_options.as_grid} |
42 }, | 41 }, |
43 width_subplot: '${output_options.width_subplot}', | 42 width_subplot: '${output_options.width_subplot}', |
65 <section name="output_options" title="Output options"> | 64 <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"> | 65 <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> | 66 <option value="pdf">Pdf</option> |
68 <option value="svg">Svg</option> | 67 <option value="svg">Svg</option> |
69 </param> | 68 </param> |
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> | |
70 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots" | 73 <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."/> | 74 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" | 75 <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."/> | 76 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" | 77 <param name="width_subplot" type="float" min="1.0" max="15.0" value="4.0" label="width of subfig plots" |
101 <section name="output_options"> | 104 <section name="output_options"> |
102 <param name="alpha" value="1.0"/> | 105 <param name="alpha" value="1.0"/> |
103 <param name="height_subplot" value="6.4"/> | 106 <param name="height_subplot" value="6.4"/> |
104 <param name="width_subplot" value="4.0"/> | 107 <param name="width_subplot" value="4.0"/> |
105 <param name="xaxis_title" value="Time"/> | 108 <param name="xaxis_title" value="Time"/> |
109 <param name="color_lines_by" value="condition"/> | |
106 <param name="figure_format" value="svg"/> | 110 <param name="figure_format" value="svg"/> |
107 </section> | 111 </section> |
108 | 112 |
109 <output_collection name="report" type="list" count="6"> | 113 <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"/> | 114 <element file="mean_enrichment-cell-Fumaric_acid.svg" name="mean_enrichment-cell-Fumaric_acid" ftype="svg" compare="sim_size" delta="100"/> |
225 | 229 |
226 **Available data for testing** | 230 **Available data for testing** |
227 | 231 |
228 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent | 232 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). | 233 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 | 234 You can also use the minimal data examples from https://zenodo.org/record/8380706 |
231 | 235 |
232 ]]> | 236 ]]> |
233 </help> | 237 </help> |
234 <expand macro="citations"/> | 238 <expand macro="citations"/> |
235 </tool> | 239 </tool> |