comparison dimet_differential_analysis.xml @ 2:e45e03a99d56 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f

1:dc199abf3db4

    <command detect_errors="exit_code"><![CDATA[
    @INIT_CONFIG@
    @INIT_DIFF_ANALYSIS@
    @INIT_STAT_TEST@
    @INIT_GROUPS@
    @INIT_COMPARISONS@
    HYDRA_FULL_ERROR=1 python -m dimet
        -cp '$__new_file_path__/config'
        '++hydra.run.dir=differential_analysis'
        '++figure_path=figures'
        '++table_path=tables'

         '++analysis.method.grouping=${groups}'
         '++analysis.method.correction_method=${correction_method}'
         '++analysis.method.impute_values=${impute_values}'
         '++analysis.statistical_test=${statistical_test}'
         '++analysis.dataset.subfolder='
         '++analysis.dataset.conditions=${conds}'
         #if $metadata_path:
             '++analysis.dataset.metadata=metadata'
         #end if
         #if str( $data_input.data_input_selector ) == "abundance":
            #if $data_input.abundance_file:

        #end if
    @REMOVE_CONFIG@
    ]]></command>
    <inputs>
        <expand macro="input_parameters_diff_analysis"/>
        <expand macro="conditions"/>
        <expand macro="timepoint"/>
        <expand macro="correction_method"/>
        <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."/>
    </inputs>

        <test>
            <param name="data_input_selector" value="abundance" />
            <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
            <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
            <param name="correction_method" value="bonferroni"/>
            <param name="stat_test" value="Tt"/>
            <param name="qualityDistanceOverSpan" value="-0.3"/>
            <param name="conditions" value='Control,L-Cycloserine'/>
            <param name="timepoint" value='T0,T2h'/>
             <output_collection name="report" type="list" count="4">
                <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv"  name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
                <element file="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/>
                <element file="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>

- **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).

There exist hints on use that will guide you, next to the parameters.


**Available data for testing**

You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent
files for you are located in the subfolders inside the data folder).
You can also use the minimal data examples from https://zenodo.org/record/8380706

 ]]>
    </help>
    <expand macro="citations" />
</tool>

2:e45e03a99d56

    <command detect_errors="exit_code"><![CDATA[
    @INIT_CONFIG@
    @INIT_DIFF_ANALYSIS@
    @INIT_STAT_TEST@
    @INIT_GROUPS@
    @INIT_DIFF_ANALYSIS_COMPARISONS@
    HYDRA_FULL_ERROR=1 python -m dimet
        -cp '$__new_file_path__/config'
        '++hydra.run.dir=differential_analysis'
        '++figure_path=figures'
        '++table_path=tables'

         '++analysis.method.grouping=${groups}'
         '++analysis.method.correction_method=${correction_method}'
         '++analysis.method.impute_values=${impute_values}'
         '++analysis.statistical_test=${statistical_test}'
         '++analysis.dataset.subfolder='
         '++analysis.dataset.conditions=${conditions}'
         #if $metadata_path:
             '++analysis.dataset.metadata=metadata'
         #end if
         #if str( $data_input.data_input_selector ) == "abundance":
            #if $data_input.abundance_file:

        #end if
    @REMOVE_CONFIG@
    ]]></command>
    <inputs>
        <expand macro="input_parameters_diff_analysis"/>
        <expand macro="factor_list"/>
        <expand macro="timepoint"/>
        <expand macro="correction_method"/>
        <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."/>
    </inputs>

        <test>
            <param name="data_input_selector" value="abundance" />
            <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>
            <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>
            <param name="correction_method" value="bonferroni"/>
            <param name="statistical_test_type" value="parametric"/>
            <param name="stat_test" value="Tt"/>
            <param name="qualityDistanceOverSpan" value="-0.3"/>
            <repeat name="factor_list">
                <param name="condition" value="Control"/>
            </repeat>
            <repeat name="factor_list">
                <param name="condition" value="L-Cycloserine"/>
            </repeat>
            <param name="timepoint" value='T0,T2h'/>
             <output_collection name="report" type="list" count="4">
                <element file="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv"  name="abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>
                <element file="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" name="abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv" ftype="tabular"/>
                <element file="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" name="abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv" ftype="tabular"/>

- **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).

There exist hints on use that will guide you, next to the parameters.

For more information about the implemented statistical tests, please visit:  https://github.com/cbib/DIMet/wiki/2-Statistical-tests

The output files are explained in https://github.com/cbib/DIMet/wiki/3-Output



**Available data for testing**

You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent
files for you are located in the subfolders inside the data folder).
You can also use the minimal data examples from https://zenodo.org/record/10579891

 ]]>
    </help>
    <expand macro="citations" />
</tool>