--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maaslin3.xml	Thu Jan 22 09:52:09 2026 +0000
@@ -0,0 +1,537 @@
+<tool id="maaslin3" name="MaAsLin3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Microbiome Multivariable Association with Linear Models</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+            mkdir 'output' &&
+
+            #if $fixed_effects:
+                #set idx = []
+                #for $i in $fixed_effects:
+                    #silent idx.append(f'${i}')
+                #end for
+                #set idx_for_awk = ','.join(idx)
+
+                fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk }' "$input_metadata"` &&
+                echo 'Assigned fixed effects as:' \$fixed_effects &&
+            #end if
+
+            #if $random_effects:
+            #set idx = []
+            #for $i in $random_effects:
+                #silent idx.append(f'${i}')
+            #end for
+            #set idx_for_awk = ','.join(idx)
+
+            random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk }' "$input_metadata"` &&
+            echo 'Assigned random effects as:' \$random_effects &&
+            #end if
+
+            #if $group_effects:
+                #set idx = []
+                #for $i in $group_effects:
+                    #silent idx.append(f'${i}')
+                #end for
+                #set idx_for_awk = ','.join(idx)
+
+                group_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk }' "$input_metadata"` &&
+                echo 'Assigned group effects as:' \$group_effects &&
+            #end if
+
+            #if $ordered_effects:
+                #set idx = []
+                #for $i in $ordered_effects:
+                    #silent idx.append(f'${i}')
+                #end for
+                #set idx_for_awk = ','.join(idx)
+
+                ordered_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk }' "$input_metadata"` &&
+                echo 'Assigned fixed effects as:' \$ordered_effects &&
+            #end if
+
+            #if $strata_effects:
+                strata_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $strata_effects }' "$input_metadata"` &&
+                echo 'Assigned strata effects as:' \$strata_effects &&
+            #end if
+
+            #if $covariate.feature_specific_covariate and $covariate.feature_specific_covariate_name:
+                #set idx = []
+                #for $i in $covariate.feature_specific_covariate_name:
+                    #silent idx.append(f'${i}')
+                #end for
+                #set idx_for_awk = ','.join(idx)
+
+                covariate.feature_specific_covariate_name=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk }' "$covariate.feature_specific_covariate"` &&
+                echo 'Assigned covariate feature specific covariate name as:' \$covariate.feature_specific_covariate_name &&
+            #end if
+
+            #if len($ref) != 0:
+                #set ref_dict = []
+                #for $i, $r in enumerate($ref):
+                    #silent $ref_dict.append('%s' %(str($r.reference)))
+                #end for
+                #set final_ref = ';'.join(ref_dict)
+            #end if
+
+            ln -s '$input_data' 'input_data.tsv' &&
+            ln -s '$input_metadata' 'input_metadata.tsv' &&
+
+            #if $options.unscaled_abundance:
+                ln -s '$options.unscaled_abundance' 'unscaled_abundance.tsv' &&
+            #end if
+
+            #if $covariate.feature_specific_covariate:
+                ln -s '$covariate.feature_specific_covariate' 'feature_specific_covariate.tsv' &&
+            #end if
+
+            maaslin3.R
+            'input_data.tsv'
+            'input_metadata.tsv'
+            'output'
+            #if $formula:
+                --formula  '~ $formula'
+            #end if
+            #if $fixed_effects:
+                --fixed_effects \$fixed_effects
+            #end if
+            #if len($ref) != 0:
+                --reference '$final_ref'
+            #end if
+            #if $random_effects:
+                --random_effects \$random_effects
+            #end if
+            #if $group_effects:
+                --group_effects \$group_effects
+            #end if
+            #if $ordered_effects:
+                --ordered_effects \$ordered_effects
+            #end if
+            #if $strata_effects:
+                --strata_effects  \$strata_effects
+            #end if
+            #if $options.min_abundance:
+                --min_abundance ${options.min_abundance}
+            #end if
+            #if $options.min_prevalence:
+                --min_prevalence ${options.min_prevalence}
+            #end if
+            #if $options.zero_threshold:
+                --zero-threshold ${options.zero_threshold}
+            #end if
+            #if $options.min_variance:
+                --min_variance ${options.min_variance}
+            #end if
+            #if $options.max_significance:
+                --max_significance $options.max_significance
+            #end if
+            --normalization '$options.normalization'
+            --transform '$options.transform'
+            --correction '$options.correction'
+            ${options.standardize}
+            #if $options.unscaled_abundance:
+                --unscaled_abundance 'unscaled_abundance.tsv'
+            #end if
+            ${options.median_comparison_abundance}
+            ${options.median_comparison_prevalence}
+            #if $options.median_comparison_abundance_threshold:
+                --median_comparison_abundance_threshold ${options.median_comparison_abundance_threshold}
+            #end if
+            #if $options.median_comparison_prevalence_threshold:
+                --median_comparison_prevalence_threshold ${options.median_comparison_prevalence_threshold}
+            #end if
+            ${options.subtract_median}
+            ${options.warn_prevalence}
+            ${options.small_random_effects}
+            ${options.augment}
+            #if $options.evaluate_only != 'NULL':
+                --evaluate_only '$options.evaluate_only'
+            #end if
+            #if $covariate.feature_specific_covariate:
+                --feature_specific_covariate 'feature_specific_covariate.tsv'
+            #end if
+            #if $covariate.feature_specific_covariate and $covariate.feature_specific_covariate_name:
+                --feature_specific_covariate_name \$covariate.feature_specific_covariate_name
+            #end if
+            #if $covariate.feature_specific_covariate and $covariate.feature_specific_covariate_record:
+                --feature_specific_covariate_record '$covariate.feature_specific_covariate_record'
+            #end if
+            ${output.plot_summary_plot}
+            #if $output.summary_plot_first_n:
+                --summary_plot_first_n ${output.summary_plot_first_n}
+            #end if
+            #if $output.coef_plot_vars:
+                --coef_plot_vars '$output.coef_plot_vars'
+            #end if
+            #if $output.heatmap_vars:
+                --heatmap_vars '$output.heatmap_vars'
+            #end if
+            ${output.plot_associations}
+            #if $output.max_pngs:
+                --max_pngs ${output.max_pngs}
+            #end if
+            ${output.save_models}
+            ${output.save_plots_rds}
+            ${output.summary_plot_balanced}
+            --cores "\${GALAXY_SLOTS:-1}"
+    ]]></command>
+    <inputs>
+        <param name="input_data" type="data" format="tabular" label="Data file"/>
+        <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
+        <param argument="--formula" type="text" value="" label="Input formula (use header of columns for this)" help="Enter the formula which should the model use. NOTE: separate the name with and plus and have space between it like: 'header1 + header2 + ...' as an example. When no input is used all columns will be used"/>
+        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set fix effects" help="Select the fix effects for the model. DEFAULT: ALL"/>
+        <repeat name="ref" title="Reference pairs">
+            <param argument="--reference" type="text" label="Reference" help="The factor to use as a reference for a variable with more than two levels provided as a string of 'variable,reference'. DEFAULT: NA"/>
+        </repeat>
+        <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set random effects" help="Select the random effects for the model. DEFAULT; NONE"/>
+        <param argument="--group_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set group effects" help="Select group effects for the model. DEFAULT: NONE"/>
+        <param argument="--ordered_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set ordered effects" help="Select the ordered effects for the model. DEFAULT: NONE"/>
+        <param argument="--strata_effects" type="data_column" data_ref="input_metadata" use_header_names="true" optional="true" label="Set strata effects" help="Select only one strata effect for the model. DEFAULT: NONE"/>
+        <section name="options" title="Additional options" expanded="true">
+            <param argument="--min_abundance" type="integer" value="0" label="Minimum abundance" help="Minimum abundance for each feature befor normalization and transformation"/>
+            <param argument="--min_prevalence" type="integer" value="0" label="Mimimum prevalence" help="The minimum proportion of samples for which a feature is detected at minimum abundance"/>
+            <param argument="--zero-threshold" type="integer" value="0" label="Zero threshold" help="The minimum abundance to be considered non-zero"/>
+            <param argument="--min_variance" type="integer" value="0" label="Minimum variance" help="Keep features with variances greater than value"/>
+            <param argument="--max_significance" type="float" value="0.1" label="Maximum significance" help="The q-value threshold for significance"/>
+            <param argument="--normalization" type="select" label="Normalization method">
+                <option value="TSS" selected="true">TSS</option>
+                <option value="CLR">CLR</option>
+                <option value="NONE">NONE</option>
+            </param>
+            <param argument="--transform" type="select" label="Transform to apply">
+                <option value="LOG" selected="true">LOG</option>
+                <option value="PLOG">PLOG</option>
+                <option value="NONE">NONE</option>
+            </param>
+            <param argument="--correction" type="select" label="correction method for computing the q-value">
+                <option value="BH" selected="true">BH</option>
+                <option value="BY">BY</option>
+                <option value="bonferroni">bonferroni</option>
+                <option value="holm">holm</option>
+                <option value="hochberg">hochberg</option>
+                <option value="hommel">hommel</option>
+                <option value="fdr">fdr</option>
+                <option value="none">none</option>
+            </param>
+            <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="" checked="true" label="Standardize" help="Scale continuous metadata witth the z-score(converting the interpretation of its scale for a standardized scale)"/>
+            <param argument="--unscaled_abundance" type="data" format="tabular" optional="true" label="unscaled abundance reference table" help="The table to use as an unscaled abundance reference. Example in the help section. NOTE: the single column name must be the same as one of the features or 'total'!"/>
+            <param argument="--median_comparison_abundance" type="boolean" truevalue="--median_comparison_abundance TRUE" falsevalue="" checked="true" label="Median comparison abundance" help="Test abundance coefficients against the median association"/>
+            <param argument="--median_comparison_prevalence" type="boolean" truevalue="--median_comparison_prevalence TRUE" falsevalue="--median_comparison_prevalence FALSE" checked="false" label="Median comparison prevalence" help="Test prevalence coefficients against the median association"/>
+            <param argument="--median_comparison_abundance_threshold" type="integer" value="0" label="Median comparison abundance threshold" help="Radius within which the median adjustment gives a p-value of 1"/>
+            <param argument="--median_comparison_prevalence_threshold" type="integer" value="0" label="Median comparison prevalence threshold" help="Radius within which the median adjustment gives a p-value of 1"/>
+            <param argument="--subtract_median" type="boolean" truevalue="--subtract_median TRUE" falsevalue="--subtract_median FALSE" checked="false" label="Subtract median" help="Subtract the median from coefficients when doing median comparisons"/>
+            <param argument="--warn_prevalence" type="boolean" truevalue="--warn_prevalence TRUE" falsevalue="" checked="true" label="Warn prevalence" help="Check and warn if prevalence associations are likely due to compositionality"/>
+            <param argument="--small_random_effects" type="boolean" truevalue="--small_random_effects TRUE" falsevalue="--small_random_effects FALSE" checked="false" label="Small random effects" help=" Replace prevalence random effects with fixed effects because groups are small"/>
+            <param argument="--augment" type="boolean" truevalue="--augment TRUE" falsevalue="--augment FALSE" checked="true" label="Augment" help="Add weighted extra 0s and 1s to avoid linear separability"/>
+            <param argument="--evaluate_only" type="select" label="Evaluate only" help="Whether to evaluate just the abundnace or prevalence models">
+                <option value="NULL" selected="true">NULL</option>
+                <option value="none">None</option>
+                <option value="abundance">abundance</option>
+                <option value="prevalence">prevalence</option>
+            </param>
+        </section>
+        <section name="covariate" title="Feature specific covariate">
+            <param argument="--feature_specific_covariate" type="data" format="tabular" optional="true" label="feature-specific covariates table" help="The table to use for feature-specific covariates. Row and column names should match the data input. EXAMPLE IN THE HELP SECTION DOWN BELOW!"/>
+            <param argument="--feature_specific_covariate_name" type="data_column" data_ref="feature_specific_covariate" use_header_names="true" multiple="true" optional="true" label="Set feature-specific covariate" help="Select the feature-specific covariate"/>
+            <param argument="--feature_specific_covariate_record" type="text" optional="true" label="Set feature_specific_covariate data" help="Select which data (rows) should included for the feature-specific covariate"/>
+        </section>
+        <section name="output" title="Output options">
+            <param argument="--plot_summary_plot" type="boolean" truevalue="--plot_summary_plot TRUE" falsevalue="--plot_summary_plot FALSE" checked="true" label="Plot summary plot"/>
+            <param argument="--summary_plot_first_n" type="integer" value="25" label="Summary plot first n" help="In summary plot, plot top N features with significant associations"/>
+            <param argument="--coef_plot_vars" type="text" label="Coefficient plot variables" help="The variables to use in the coefficient plot section of the summary plot provided as a comma-separated string. Continuous variables should match the metadata column name, and categorical variables should be of the form: [metadata] [level]. DEFAULT: NA"/>
+            <param argument="--heatmap_vars" type="text" label="Heatmap variables" help="The variables to use in the heatmap section of the summary plot provided as a comma-separated string. Continuous variables should match the metadata column name, and categorical variables should be of the form: [metadata] [level]. DEFAULT: NA"/>
+            <param argument="--plot_associations" type="boolean" truevalue="--plot_associations TRUE" falsevalue="--plot_associations FALSE" checked="true" label="Plot associations"/>
+            <param argument="--max_pngs" type="integer" value="30" label=" maximum number of association plots"/>
+            <param argument="--save_models" type="boolean" truevalue="--save_models TRUE" falsevalue="--save_models FALSE" checked="false" label="Save model" help="Return the full model outputs and save to an RData file"/>
+            <param argument="--save_plots_rds" type="boolean" truevalue="--save_plots_rds TRUE" falsevalue="--save_plots_rds FALSE" checked="false" label="Save plots as rds" help="Save the plots to RDS files"/>
+            <param argument="--summary_plot_balanced" type="boolean" truevalue="--summary_plot_balanced TRUE" falsevalue="--summary_plot_balanced FALSE" checked="false" label="Summary plot balanced" help="If coef_plot_vars is selected this will select balanced top features"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="data_norm" format="tabular" from_work_dir="output/features/data_norm.tsv" label="${tool.name} on ${on_string}: DATA NORMALIZED"/>
+        <data name="data_trans" format="tabular" from_work_dir="output/features/data_transformed.tsv" label="${tool.name} on ${on_string}: DATA TRANSFORMED"/>
+        <data name="data_filter" format="tabular" from_work_dir="output/features/filtered_data.tsv" label="${tool.name} on ${on_string}: FILTERED DATA"/>
+        <collection name="rdata" type="list" label="${tool.name} on ${on_string}: R DATA">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="output/fits" format="rdata"/>
+        </collection>
+        <collection name="plots" type="list:list" label="${tool.name} on ${on_string}: PLOTS">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" directory="output/figures/association_plots" recurse="true" format="png"/>
+            <filter>output['plot_associations'] is True</filter>
+        </collection>
+        <data name="summary_png" format="png" from_work_dir="output/figures/summary_plot.png" label="${tool.name} on ${on_string}: SUMMARY PLOT (PNG)">
+            <filter>output['summary_plot_balanced'] is False</filter>
+        </data>
+        <data name="summary_pdf" format="pdf" from_work_dir="output/figures/summary_plot.pdf" label="${tool.name} on ${on_string}: SUMMARY PLOT (PDF)">
+            <filter>output['summary_plot_balanced'] is False</filter>
+        </data>
+        <collection name="plots_r" type="list" label="${tool.name} on ${on_string}: PLOTS (R DATA)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.RDS" directory="output/figures" recurse="true" format="rdata"/>
+            <filter>output['plot_associations'] is True and output['save_plots_rds'] is True</filter>
+        </collection>
+        <data name="result_all" format="tabular" from_work_dir="output/all_results.tsv" label="${tool.name} on ${on_string}: ALL RESULT"/>
+        <data name="result_sig" format="tabular" from_work_dir="output/significant_results.tsv" label="${tool.name} on ${on_string}: SIGNIFICANT RESULT"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="9">
+            <param name="input_data" value="HMP2_taxonomy.tsv" ftype="tabular"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv" ftype="tabular"/>
+            <param name="formula" value="reads + diagnosis + dysbiosis_state + antibiotics + age"/>
+            <repeat name="ref">
+                <param name="reference" value="diagnosis,CD"/>
+            </repeat>
+            <repeat name="ref">
+                <param name="reference" value="dysbiosis_state,dysbiosis_UC"/>
+            </repeat>
+            <output name="data_norm" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="data_trans" file="data_transformed.tsv" ftype="tabular"/>
+            <output name="data_filter" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output_collection name="rdata" type="list">
+                <element name="fitted_linear.rds" ftype="rdata">
+                    <assert_contents>
+                        <has_size value="327196" delta="5000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="summary_png" ftype="png">
+                <assert_contents>
+                    <has_image_height height="3690" delta="20"/>
+                    <has_image_width width="4375" delta="20"/>
+                </assert_contents>
+            </output>
+            <output name="summary_pdf" ftype="pdf">
+                <assert_contents>
+                    <has_size size="18000" delta="2000"/>
+                </assert_contents>
+            </output>
+            <output name="result_all" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2036" delta="30"/>
+                </assert_contents>
+            </output>
+            <output name="result_sig" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="834" delta="15"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="7">
+            <param name="input_data" value="HMP2_taxonomy.tsv" ftype="tabular"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv" ftype="tabular"/>
+            <param name="formula" value="reads + diagnosis + dysbiosis_state + antibiotics + age"/>
+            <repeat name="ref">
+                <param name="reference" value="diagnosis,CD"/>
+            </repeat>
+            <repeat name="ref">
+                <param name="reference" value="dysbiosis_state,dysbiosis_UC"/>
+            </repeat>
+            <section name="output">
+                <param name="summary_plot_balanced" value="True"/>
+            </section>
+            <output name="data_norm" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="data_trans" file="data_transformed.tsv" ftype="tabular"/>
+            <output name="data_filter" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output_collection name="rdata" type="list">
+                <element name="fitted_linear.rds" ftype="rdata">
+                    <assert_contents>
+                        <has_size value="327196" delta="5000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="result_all" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2036" delta="30"/>
+                </assert_contents>
+            </output>
+            <output name="result_sig" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="834" delta="15"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="10">
+            <param name="input_data" value="HMP2_taxonomy.tsv" ftype="tabular"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv" ftype="tabular"/>
+            <param name="formula" value="reads + diagnosis + dysbiosis_state + antibiotics + age"/>
+            <repeat name="ref">
+                <param name="reference" value="diagnosis,CD"/>
+            </repeat>
+            <repeat name="ref">
+                <param name="reference" value="dysbiosis_state,dysbiosis_UC"/>
+            </repeat>
+            <section name="output">
+                <param name="save_plots_rds" value="True"/>
+            </section>
+            <output name="data_norm" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="data_trans" file="data_transformed.tsv" ftype="tabular"/>
+            <output name="data_filter" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output_collection name="rdata" type="list">
+                <element name="fitted_linear.rds" ftype="rdata">
+                    <assert_contents>
+                        <has_size value="327196" delta="5000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="summary_png" ftype="png">
+                <assert_contents>
+                    <has_image_height height="3690" delta="20"/>
+                    <has_image_width width="4375" delta="20"/>
+                </assert_contents>
+            </output>
+            <output name="summary_pdf" ftype="pdf">
+                <assert_contents>
+                    <has_size size="18000" delta="2000"/>
+                </assert_contents>
+            </output>
+            <output name="result_all" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2036" delta="30"/>
+                </assert_contents>
+            </output>
+            <output name="result_sig" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="834" delta="15"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots_r" type="list" count="4">
+                <element name="summary_plot_gg" ftype="rdata">
+                    <assert_contents>
+                        <has_size size="720000" delta="100000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="8">
+            <param name="input_data" value="HMP2_taxonomy.tsv" ftype="tabular"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv" ftype="tabular"/>
+            <param name="formula" value="reads + diagnosis + dysbiosis_state + antibiotics + age"/>
+            <repeat name="ref">
+                <param name="reference" value="diagnosis,CD"/>
+            </repeat>
+            <repeat name="ref">
+                <param name="reference" value="dysbiosis_state,dysbiosis_UC"/>
+            </repeat>
+            <section name="output">
+                <param name="save_models" value="True"/>
+                <param name="plot_associations" value="False"/>
+            </section>
+            <output name="data_norm" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="data_trans" file="data_transformed.tsv" ftype="tabular"/>
+            <output name="data_filter" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="818" delta="10"/>
+                </assert_contents>
+            </output>
+            <output_collection name="rdata" type="list">
+                <element name="fitted_linear.rds" ftype="rdata">
+                    <assert_contents>
+                        <has_size value="327196" delta="5000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="summary_png" ftype="png">
+                <assert_contents>
+                    <has_image_height height="3690" delta="20"/>
+                    <has_image_width width="4375" delta="20"/>
+                </assert_contents>
+            </output>
+            <output name="summary_pdf" ftype="pdf">
+                <assert_contents>
+                    <has_size size="18000" delta="2000"/>
+                </assert_contents>
+            </output>
+            <output name="result_all" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2036" delta="30"/>
+                </assert_contents>
+            </output>
+            <output name="result_sig" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="834" delta="15"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+
+            **IMPORTANT**
+
+            random_effects, group_effects, ordered_effects, and strata_effects must be NULL when formula is not NULL!!
+
+            If warn_prevalence (Warn prevalence) is set to True please selecet evaluate_only (Evaluate only) to NULL.
+            If you want to use evaluate_only (Evaluate only) please do not set warn_prevalence (Warn prevalence) to True!
+            Both argument can not be set at the same time!
+
+
+            **Input**
+
+            - A data table
+            - A metadata table
+            - unscaled abundance reference table (optional)
+
+                Example::
+                    SampleID	total
+                    S1	2.3e8
+                    S2	1.8e8
+                    S3	3.1e8
+                    S4	2.6e8
+                
+                For a none specific case and here is a example for a specific case with *SpikeIn1*::
+
+                    SampleID	SpikeIn1
+                    S1	1000
+                    S2	2000
+                    S3	1500
+                    S4	1800
+            
+            - A feature-specific covariates table (optional)
+
+                Example::
+                    Feature	GC_content	Batch_flag
+                    GeneA	0.42	1
+                    GeneB	0.65	0
+                    PathwayX	NA	1
+                    PathwayY	0.58	1
+
+            **Output**
+
+            - multiple plots (optional)
+            - Plots in R format (optional)
+            - certain R format data files (some optional)
+            - Mulitple data tables
+
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1101/2024.12.13.628459</citation>
+    </citations>
+</tool>