Mercurial > repos > iuc > dimet_enrichment_plot

comparison dimet_enrichment_plot.xml @ 2:2de209fb390b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
author iuc
date Thu, 15 Feb 2024 12:52:26 +0000
parents 79720105f8c0
children be19aa1df5af
comparison
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1:79720105f8c0 2:2de209fb390b
9 </macros> 9 </macros>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @INIT_CONFIG@ 12 @INIT_CONFIG@
13 @INIT_ENRICHMENT_PLOT@ 13 @INIT_ENRICHMENT_PLOT@
14 @INIT_CONDITIONS@ 14 @INIT_PLOT_CONDITIONS@
15 @INIT_TIMEPOINTS@ 15 @INIT_TIMEPOINTS@
16 @INIT_ENRICHMENT_METABOLITES@ 16 @INIT_ENRICHMENT_METABOLITES@
17 HYDRA_FULL_ERROR=1 python -m dimet 17 HYDRA_FULL_ERROR=1 python -m dimet
18 -cp '$__new_file_path__/config' 18 -cp '$__new_file_path__/config'
19 '++hydra.run.dir=mean_enrichment_line_plot' 19 '++hydra.run.dir=mean_enrichment_line_plot'
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 palette_condition: muted, 32 palette_condition: ${output_options.palette},
33 palette_metabolite: auto_multi_color, 33 palette_metabolite: auto_multi_color,
34 xaxis_title: ${output_options.xaxis_title}, 34 xaxis_title: ${output_options.xaxis_title},
35 alpha: ${output_options.alpha}, 35 alpha: ${output_options.alpha},
36 plot_grouped_by_dict: null, 36 plot_grouped_by_dict: null,
37 color_lines_by: '${output_options.color_lines_by}', 37 color_lines_by: '${output_options.color_lines_by}',
43 label: enrich_lineplot 43 label: enrich_lineplot
44 }' 44 }'
45 '++analysis.dataset.label=' 45 '++analysis.dataset.label='
46 '++analysis.timepoints=${timepoints}' 46 '++analysis.timepoints=${timepoints}'
47 '++analysis.dataset.subfolder=' 47 '++analysis.dataset.subfolder='
48 '++analysis.dataset.conditions=${conds}' 48 '++analysis.dataset.conditions=${conditions}'
49 49
50 #if $metadata_path: 50 #if $metadata_path:
51 '++analysis.dataset.metadata=metadata' 51 '++analysis.dataset.metadata=metadata'
52 #end if 52 #end if
53 #if $me_or_frac_contrib_file: 53 #if $me_or_frac_contrib_file:
55 #end if 55 #end if
56 @REMOVE_CONFIG@ 56 @REMOVE_CONFIG@
57 ]]></command> 57 ]]></command>
58 <inputs> 58 <inputs>
59 <expand macro="input_parameters_enrichment"/> 59 <expand macro="input_parameters_enrichment"/>
60 <expand macro="conditions"/> 60 <expand macro="plot_factor_list"/>
61 <expand macro="timepoint"/> 61 <expand macro="timepoint"/>
62 <expand macro="compartments_enrichment"/> 62 <expand macro="compartments_enrichment"/>
63 <expand macro="enrichment_metabolites_list"/> 63 <expand macro="enrichment_metabolites_list"/>
64 <section name="output_options" title="Output options"> 64 <section name="output_options" title="Output options">
65 <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">
66 <option value="pdf">Pdf</option> 66 <option value="pdf">Pdf</option>
67 <option value="svg">Svg</option> 67 <option value="svg">Svg</option>
68 </param> 68 </param>
69 <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 <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="condition">Condition</option>
71 <option value="metabolite">Metabolite</option> 72 <option value="metabolite">Metabolite</option>
72 </param> 73 </param>
73 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots" 74 <param name="alpha" type="float" min="0.0" max="1.0" value="1.0" label="alpha of subfig plots"
95 </outputs> 96 </outputs>
96 <tests> 97 <tests>
97 <test> 98 <test>
98 <param name="me_or_frac_contrib_file" ftype="tabular" value="FracContribution_C.csv"/> 99 <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 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
100 <param name="conditions" value='Control,L-Cycloserine'/> 101 <repeat name="plot_factor_list">
102 <param name="condition" value="Control"/>
103 </repeat>
104 <repeat name="plot_factor_list">
105 <param name="condition" value="L-Cycloserine"/>
106 </repeat>
101 <param name="timepoint" value='T0,T2h'/> 107 <param name="timepoint" value='T0,T2h'/>
102 <param name="compartments" value='cell,med'/> 108 <param name="compartments" value='cell,med'/>
103 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/> 109 <param name="metabolites_list" value="Fumaric_acid,Glycine,L-Proline"/>
104 <section name="output_options"> 110 <section name="output_options">
105 <param name="alpha" value="1.0"/> 111 <param name="alpha" value="1.0"/>
227 233
228 The output consists of line-plot figures, one by each metabolite. 234 The output consists of line-plot figures, one by each metabolite.
229 235
230 **Available data for testing** 236 **Available data for testing**
231 237
232 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent 238 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
233 files for you are located in the subfolders inside the data folder). 239 files for you are located in the subfolders inside the data folder).
234 You can also use the minimal data examples from https://zenodo.org/record/8380706 240 You can also use the minimal data examples from https://zenodo.org/record/10579891
235 241
236 ]]> 242 ]]>
237 </help> 243 </help>
238 <expand macro="citations"/> 244 <expand macro="citations"/>
239 </tool> 245 </tool>