Mercurial > repos > iuc > dimet_timecourse_analysis

comparison dimet_timecourse_analysis.xml @ 2:40edef7d7f74 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
author iuc
date Thu, 15 Feb 2024 12:50:27 +0000
parents cb8c4ae59da9
children b856fcb1346e
comparison
equal deleted inserted replaced
1:b97f326c055d 2:40edef7d7f74
37 '++analysis.method.grouping=${groups}' 37 '++analysis.method.grouping=${groups}'
38 '++analysis.method.correction_method=${correction_method}' 38 '++analysis.method.correction_method=${correction_method}'
39 '++analysis.method.impute_values=${impute_values}' 39 '++analysis.method.impute_values=${impute_values}'
40 '++analysis.dataset.subfolder=' 40 '++analysis.dataset.subfolder='
41 '++analysis.dataset.label=' 41 '++analysis.dataset.label='
42 '++analysis.dataset.conditions=${conds}' 42 '++analysis.dataset.conditions=${conditions}'
43 #if $metadata_path: 43 #if $metadata_path:
44 '++analysis.dataset.metadata=metadata' 44 '++analysis.dataset.metadata=metadata'
45 #end if 45 #end if
46 #if str( $data_input.data_input_selector ) == "abundance": 46 #if str( $data_input.data_input_selector ) == "abundance":
47 #if $data_input.abundance_file: 47 #if $data_input.abundance_file:
62 #end if 62 #end if
63 @REMOVE_CONFIG@ 63 @REMOVE_CONFIG@
64 ]]></command> 64 ]]></command>
65 <inputs> 65 <inputs>
66 <expand macro="input_parameters_diff_analysis"/> 66 <expand macro="input_parameters_diff_analysis"/>
67 <expand macro="conditions"/> 67 <expand macro="factor_list"/>
68 <expand macro="correction_method"/> 68 <expand macro="correction_method"/>
69 <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/> 69 <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>
70 </inputs> 70 </inputs>
71 <outputs> 71 <outputs>
72 <collection name="report" type="list"> 72 <collection name="report" type="list">
78 <param name="data_input_selector" value="abundance" /> 78 <param name="data_input_selector" value="abundance" />
79 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/> 79 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
80 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> 80 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
81 <param name="correction_method" value="bonferroni"/> 81 <param name="correction_method" value="bonferroni"/>
82 <param name="qualityDistanceOverSpan" value="-0.3"/> 82 <param name="qualityDistanceOverSpan" value="-0.3"/>
83 <param name="statistical_test_type" value="parametric"/>
83 <param name="stat_test" value="Tt"/> 84 <param name="stat_test" value="Tt"/>
84 <param name="conditions" value='Control,L-Cycloserine'/> 85 <repeat name="plot_factor_list">
86 <param name="condition" value="Control"/>
87 </repeat>
88 <repeat name="plot_factor_list">
89 <param name="condition" value="L-Cycloserine"/>
90 </repeat>
85 <output_collection name="report" type="list" count="4"> 91 <output_collection name="report" type="list" count="4">
86 <element file="abundance--cell-Control-T2h-Control-T0-Tt.tsv" name="abundance--cell-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/> 92 <element file="abundance--cell-Control-T2h-Control-T0-Tt.tsv" name="abundance--cell-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/>
87 <element file="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> 93 <element file="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
88 <element file="abundance--med-Control-T2h-Control-T0-Tt.tsv" name="abundance--med-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/> 94 <element file="abundance--med-Control-T2h-Control-T0-Tt.tsv" name="abundance--med-Control-T2h-Control-T0-Tt.tsv" ftype="tabular"/>
89 <element file="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> 95 <element file="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" name="abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
257 There exist hints on use that will guide you, next to the parameters. 263 There exist hints on use that will guide you, next to the parameters.
258 264
259 The output consists of tables with the computed metrics, one by each pair of timepoints compared. 265 The output consists of tables with the computed metrics, one by each pair of timepoints compared.
260 The number of output tables = number-of-conditions x (number-of-timepoints)-1 x number-of-compartments. 266 The number of output tables = number-of-conditions x (number-of-timepoints)-1 x number-of-compartments.
261 267
268 For more information about the implemented statistical tests, please visit: https://github.com/cbib/DIMet/wiki/2-Statistical-tests
269
270 The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
271
262 **Available data for testing** 272 **Available data for testing**
263 273
264 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent 274 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
265 files for you are located in the subfolders inside the data folder). 275 files for you are located in the subfolders inside the data folder).
266 You can also use the minimal data examples from https://zenodo.org/record/8380706 276 You can also use the minimal data examples from https://zenodo.org/record/10579891
267 277
268 ]]> 278 ]]>
269 </help> 279 </help>
270 <expand macro="citations" /> 280 <expand macro="citations" />
271 </tool> 281 </tool>