comparison macros.xml @ 4:f8247afcd994 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit afc87f0254b4399b71e53735966032ba1a32434d

3:8579d74e740b

<macros>
    <token name="@TOOL_VERSION@">0.2.2</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@EXECUTABLE@">pca</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
        </requirements>
    </xml>
    <xml name="statistical_test_for_multigroup">
        <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">
            <option value="KW">Kruskal-Wallis</option>
        </param>
    </xml>
    <xml name="statistical_test">
        <conditional name="statistics">
            <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">

            <when value="isotop_abs">
                <expand macro="isotopologue_abs_file_macros"/>
            </when>
        </conditional>
        <expand macro="metadata_file_macros"/>
    </xml>
    <xml name="input_parameters_diff_analysis">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
                <option value="abundance" selected="True">abundance</option>

    mkdir -p data &&

    #if $metadata_path:
        ln -s '$metadata_path' data/metadata.csv &&
    #end if
    #set conditions_MDV_comparison  = {}
    #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
    #set timepoints_MDV_comparison  = {}
    #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
    #set conditions_metabolite_time_profiles  = {}
    #silent $conditions_metabolite_time_profiles['abundances']='pearson'
    #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'

    #set $impute_values  = {}
    #if str( $data_input.data_input_selector ) == "abundance":
        #if $data_input.abundance_file:
            ln -s '$data_input.abundance_file' data/abundance.csv &&
            #silent $impute_values['abundances']='min'

4:f8247afcd994

<macros>
    <token name="@TOOL_VERSION@">0.2.4</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@EXECUTABLE@">pca</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
        </requirements>
    </xml>
    <xml name="statistical_test_for_multigroup">
        <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">
            <option value="KW">Kruskal-Wallis</option>
        </param>
    </xml>
     <xml name="statistical_test_for_bivariate_analysis">
        <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">
            <option value="pearson">pearson</option>
            <option value="spearman">spearman</option>
        </param>
    </xml>
    <xml name="statistical_test">
        <conditional name="statistics">
            <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">

            <when value="isotop_abs">
                <expand macro="isotopologue_abs_file_macros"/>
            </when>
        </conditional>
        <expand macro="metadata_file_macros"/>
        <expand macro="statistical_test_for_bivariate_analysis"/>
    </xml>
    <xml name="input_parameters_diff_analysis">
        <conditional name="data_input">
            <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
                <option value="abundance" selected="True">abundance</option>

    mkdir -p data &&

    #if $metadata_path:
        ln -s '$metadata_path' data/metadata.csv &&
    #end if


    #set conditions_MDV_comparison  = {}
    #set timepoints_MDV_comparison  = {}
    #set conditions_metabolite_time_profiles  = {}

    #if str( $stat_test ) == "pearson":
        #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
        #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
        #silent $conditions_metabolite_time_profiles['abundances']='pearson'
        #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
    #else
        #silent $conditions_MDV_comparison['isotopologue_proportions']='spearman'
        #silent $timepoints_MDV_comparison['isotopologue_proportions']='spearman'
        #silent $conditions_metabolite_time_profiles['abundances']='spearman'
        #silent $conditions_metabolite_time_profiles['mean_enrichment']='spearman'
    #end if
    #set $impute_values  = {}
    #if str( $data_input.data_input_selector ) == "abundance":
        #if $data_input.abundance_file:
            ln -s '$data_input.abundance_file' data/abundance.csv &&
            #silent $impute_values['abundances']='min'