Mercurial > repos > iuc > dimet_differential_analysis

comparison dimet_differential_analysis.xml @ 2:e45e03a99d56 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 12:53:06 +0000
parents c46d33411495
children 8579d74e740b
comparison
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1:dc199abf3db4 2:e45e03a99d56
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @INIT_CONFIG@ 12 @INIT_CONFIG@
13 @INIT_DIFF_ANALYSIS@ 13 @INIT_DIFF_ANALYSIS@
14 @INIT_STAT_TEST@ 14 @INIT_STAT_TEST@
15 @INIT_GROUPS@ 15 @INIT_GROUPS@
16 @INIT_COMPARISONS@ 16 @INIT_DIFF_ANALYSIS_COMPARISONS@
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=differential_analysis' 19 '++hydra.run.dir=differential_analysis'
20 '++figure_path=figures' 20 '++figure_path=figures'
21 '++table_path=tables' 21 '++table_path=tables'
41 '++analysis.method.grouping=${groups}' 41 '++analysis.method.grouping=${groups}'
42 '++analysis.method.correction_method=${correction_method}' 42 '++analysis.method.correction_method=${correction_method}'
43 '++analysis.method.impute_values=${impute_values}' 43 '++analysis.method.impute_values=${impute_values}'
44 '++analysis.statistical_test=${statistical_test}' 44 '++analysis.statistical_test=${statistical_test}'
45 '++analysis.dataset.subfolder=' 45 '++analysis.dataset.subfolder='
46 '++analysis.dataset.conditions=${conds}' 46 '++analysis.dataset.conditions=${conditions}'
47 #if $metadata_path: 47 #if $metadata_path:
48 '++analysis.dataset.metadata=metadata' 48 '++analysis.dataset.metadata=metadata'
49 #end if 49 #end if
50 #if str( $data_input.data_input_selector ) == "abundance": 50 #if str( $data_input.data_input_selector ) == "abundance":
51 #if $data_input.abundance_file: 51 #if $data_input.abundance_file:
66 #end if 66 #end if
67 @REMOVE_CONFIG@ 67 @REMOVE_CONFIG@
68 ]]></command> 68 ]]></command>
69 <inputs> 69 <inputs>
70 <expand macro="input_parameters_diff_analysis"/> 70 <expand macro="input_parameters_diff_analysis"/>
71 <expand macro="conditions"/> 71 <expand macro="factor_list"/>
72 <expand macro="timepoint"/> 72 <expand macro="timepoint"/>
73 <expand macro="correction_method"/> 73 <expand macro="correction_method"/>
74 <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."/> 74 <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."/>
75 </inputs> 75 </inputs>
76 76
83 <test> 83 <test>
84 <param name="data_input_selector" value="abundance" /> 84 <param name="data_input_selector" value="abundance" />
85 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/> 85 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
86 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> 86 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
87 <param name="correction_method" value="bonferroni"/> 87 <param name="correction_method" value="bonferroni"/>
88 <param name="statistical_test_type" value="parametric"/>
88 <param name="stat_test" value="Tt"/> 89 <param name="stat_test" value="Tt"/>
89 <param name="qualityDistanceOverSpan" value="-0.3"/> 90 <param name="qualityDistanceOverSpan" value="-0.3"/>
90 <param name="conditions" value='Control,L-Cycloserine'/> 91 <repeat name="factor_list">
92 <param name="condition" value="Control"/>
93 </repeat>
94 <repeat name="factor_list">
95 <param name="condition" value="L-Cycloserine"/>
96 </repeat>
91 <param name="timepoint" value='T0,T2h'/> 97 <param name="timepoint" value='T0,T2h'/>
92 <output_collection name="report" type="list" count="4"> 98 <output_collection name="report" type="list" count="4">
93 <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> 99 <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
94 <element file="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/> 100 <element file="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/>
95 <element file="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/> 101 <element file="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
281 287
282 - **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html). 288 - **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html).
283 289
284 There exist hints on use that will guide you, next to the parameters. 290 There exist hints on use that will guide you, next to the parameters.
285 291
292 For more information about the implemented statistical tests, please visit: https://github.com/cbib/DIMet/wiki/2-Statistical-tests
293
294 The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output
295
296
286 297
287 **Available data for testing** 298 **Available data for testing**
288 299
289 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent 300 You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
290 files for you are located in the subfolders inside the data folder). 301 files for you are located in the subfolders inside the data folder).
291 You can also use the minimal data examples from https://zenodo.org/record/8380706 302 You can also use the minimal data examples from https://zenodo.org/record/10579891
292 303
293 ]]> 304 ]]>
294 </help> 305 </help>
295 <expand macro="citations" /> 306 <expand macro="citations" />
296 </tool> 307 </tool>