Mercurial > repos > iuc > dimet_abundance_plot

comparison dimet_abundance_plot.xml @ 2:1df18470e3d0 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 12:51:47 +0000
parents 07164270ec13
children 279ce0d93d53
comparison
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1:07164270ec13 2:1df18470e3d0
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_ABUNDANCE_PLOT@ 13 @INIT_ABUNDANCE_PLOT@
14 @INIT_CONDITIONS@ 14 @INIT_ABUNDANCE_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=abundance_plot' 19 '++hydra.run.dir=abundance_plot'
33 axisx: condition, 33 axisx: condition,
34 axisx_labeltilt: '${output_options.axisx_labeltilt}', 34 axisx_labeltilt: '${output_options.axisx_labeltilt}',
35 height_each_subfig: '${output_options.height_each_subfig}', 35 height_each_subfig: '${output_options.height_each_subfig}',
36 palette:${output_options.palette}, 36 palette:${output_options.palette},
37 as_grid:${output_options.as_grid}, 37 as_grid:${output_options.as_grid},
38 x_text_modify_as:null,
38 do_stripplot:${output_options.do_stripplot}, 39 do_stripplot:${output_options.do_stripplot},
39 figure_format:${output_options.figure_format} 40 figure_format:${output_options.figure_format}
40 }, 41 },
41 label: abundance_plot, 42 label: abundance_plot,
42 width_each_subfig: '${output_options.width_each_subfig}' 43 width_each_subfig: '${output_options.width_each_subfig}'
43 }' 44 }'
44 '++analysis.dataset.label=' 45 '++analysis.dataset.label='
45 '++analysis.timepoints=${timepoints}' 46 '++analysis.timepoints=${timepoints}'
46 '++analysis.dataset.subfolder=' 47 '++analysis.dataset.subfolder='
47 '++analysis.dataset.conditions=${conds}' 48 '++analysis.dataset.conditions=${conditions}'
48 #if $metadata_path: 49 #if $metadata_path:
49 '++analysis.dataset.metadata=metadata' 50 '++analysis.dataset.metadata=metadata'
50 #end if 51 #end if
51 #if $abundance_file: 52 #if $abundance_file:
52 '++analysis.dataset.abundances=abundance' 53 '++analysis.dataset.abundances=abundance'
53 #end if 54 #end if
54 @REMOVE_CONFIG@ 55 @REMOVE_CONFIG@
55 ]]></command> 56 ]]></command>
56 <inputs> 57 <inputs>
57 <expand macro="input_parameters_abundance"/> 58 <expand macro="input_parameters_abundance"/>
58 <expand macro="conditions"/> 59 <expand macro="plot_abundance_factor_list"/>
59 <expand macro="timepoint"/> 60 <expand macro="timepoint"/>
60 <expand macro="compartments_abundance"/> 61 <expand macro="compartments_abundance"/>
61 <expand macro="abundance_metabolites_list"/> 62 <expand macro="abundance_metabolites_list"/>
62 <section name="output_options" title="Output options"> 63 <section name="output_options" title="Output options">
63 <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot" help="Please enter at max 1 statistical test by file"> 64 <expand macro="palette"/>
64 <option value="pastel">pastel</option>
65 <option value="Set1">Set1</option>
66 <option value="Set2">Set2</option>
67 <option value="Set3">Set3</option>
68 <option value="Dark2">Dark2</option>
69 </param>
70 <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">
71 <option value="pdf">Pdf</option> 66 <option value="pdf">Pdf</option>
72 <option value="svg">Svg</option> 67 <option value="svg">Svg</option>
73 </param> 68 </param>
74 <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt" 69 <param name="axisx_labeltilt" type="integer" min="0" max="180" value="70" label="X axis label tilt"
91 </outputs> 86 </outputs>
92 <tests> 87 <tests>
93 <test> 88 <test>
94 <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/> 89 <param name="abundance_file" ftype="tabular" value="AbundanceCorrected.csv"/>
95 <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/> 90 <param name="metadata_path" ftype="tabular" value="example1_metadata.csv"/>
96 <param name="conditions" value='sgLDHA'/> 91 <repeat name="plot_abundance_factor_list">
92 <param name="condition" value="sgLDHA"/>
93 </repeat>
97 <param name="timepoint" value='T0,T24'/> 94 <param name="timepoint" value='T0,T24'/>
98 <param name="compartments" value='endo'/> 95 <param name="compartments" value='endo'/>
99 <param name="metabolites_list" value="Fru1P"/> 96 <param name="metabolites_list" value="Fru1P"/>
100 <section name="output_options"> 97 <section name="output_options">
101 <param name="axisx_labeltilt" value="70"/> 98 <param name="axisx_labeltilt" value="70"/>
221 218
222 219
223 220
224 **Available data for testing** 221 **Available data for testing**
225 222
226 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent 223 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
227 files for you are located in the subfolders inside the data folder). 224 files for you are located in the subfolders inside the data folder).
228 You can also use the minimal data examples from https://zenodo.org/record/8380706 225 You can also use the minimal data examples from https://zenodo.org/record/10579891
229 226
230 ]]> 227 ]]>
231 </help> 228 </help>
232 <expand macro="citations"/> 229 <expand macro="citations"/>
233 </tool> 230 </tool>