Mercurial > repos > iuc > dimet_isotopologues_plot

comparison macros.xml @ 4:16c64719226c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d
author iuc
date Wed, 27 Mar 2024 16:50:32 +0000
parents b761f919732d
children 89ca62980a2e
comparison
equal deleted inserted replaced
3:b761f919732d 4:16c64719226c
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.2.2</token> 2 <token name="@TOOL_VERSION@">0.2.4</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@EXECUTABLE@">pca</token> 4 <token name="@EXECUTABLE@">pca</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
8 </requirements> 8 </requirements>
9 </xml> 9 </xml>
10 <xml name="statistical_test_for_multigroup"> 10 <xml name="statistical_test_for_multigroup">
11 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> 11 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
12 <option value="KW">Kruskal-Wallis</option> 12 <option value="KW">Kruskal-Wallis</option>
13 </param>
14 </xml>
15 <xml name="statistical_test_for_bivariate_analysis">
16 <param name="stat_test" type="select" value="pearson" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
17 <option value="pearson">pearson</option>
18 <option value="spearman">spearman</option>
13 </param> 19 </param>
14 </xml> 20 </xml>
15 <xml name="statistical_test"> 21 <xml name="statistical_test">
16 <conditional name="statistics"> 22 <conditional name="statistics">
17 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform"> 23 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform">
164 <when value="isotop_abs"> 170 <when value="isotop_abs">
165 <expand macro="isotopologue_abs_file_macros"/> 171 <expand macro="isotopologue_abs_file_macros"/>
166 </when> 172 </when>
167 </conditional> 173 </conditional>
168 <expand macro="metadata_file_macros"/> 174 <expand macro="metadata_file_macros"/>
175 <expand macro="statistical_test_for_bivariate_analysis"/>
169 </xml> 176 </xml>
170 <xml name="input_parameters_diff_analysis"> 177 <xml name="input_parameters_diff_analysis">
171 <conditional name="data_input"> 178 <conditional name="data_input">
172 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files"> 179 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
173 <option value="abundance" selected="True">abundance</option> 180 <option value="abundance" selected="True">abundance</option>
636 mkdir -p data && 643 mkdir -p data &&
637 644
638 #if $metadata_path: 645 #if $metadata_path:
639 ln -s '$metadata_path' data/metadata.csv && 646 ln -s '$metadata_path' data/metadata.csv &&
640 #end if 647 #end if
648
649
641 #set conditions_MDV_comparison = {} 650 #set conditions_MDV_comparison = {}
642 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
643 #set timepoints_MDV_comparison = {} 651 #set timepoints_MDV_comparison = {}
644 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
645 #set conditions_metabolite_time_profiles = {} 652 #set conditions_metabolite_time_profiles = {}
646 #silent $conditions_metabolite_time_profiles['abundances']='pearson' 653
647 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson' 654 #if str( $stat_test ) == "pearson":
648 655 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
656 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
657 #silent $conditions_metabolite_time_profiles['abundances']='pearson'
658 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
659 #else
660 #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
661 #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
662 #silent $conditions_metabolite_time_profiles['abundances']='spearman'
663 #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
664 #end if
649 #set $impute_values = {} 665 #set $impute_values = {}
650 #if str( $data_input.data_input_selector ) == "abundance": 666 #if str( $data_input.data_input_selector ) == "abundance":
651 #if $data_input.abundance_file: 667 #if $data_input.abundance_file:
652 ln -s '$data_input.abundance_file' data/abundance.csv && 668 ln -s '$data_input.abundance_file' data/abundance.csv &&
653 #silent $impute_values['abundances']='min' 669 #silent $impute_values['abundances']='min'