--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anova_fixed.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,101 @@
+<tool id="secimtools_anova_fixed" name="Analysis of Variance (ANOVA) Fixed Effects Model"  version="@WRAPPER_VERSION@">
+    <description>- Perform a multi-way ANOVA with covariates and fixed effects.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+anova_fixed.py
+--input $input
+--design $design
+--ID $uniqID
+--factors "$factor"
+--factorTypes $factorTypes
+--out $results_table
+--flags $flags_table
+--fig $qq_plots
+--fig2 $volcano_plots
+#if $interactions
+    --interactions
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note: you need a 'sampleID' column. If not-tab separated, see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature Identifier" help="Name of the column in your wide dataset that contains unique feature identifiers."/>
+        <param name="factor" type="text" size="30" value="" label="Group(s)/Treatment(s)" help="Name of the column(s) (comma separated) in your design file that you want to use for ANOVA (ie. treatment1,treatment2,weight)."/>
+        <param name="factorTypes" type="text" size="30" value="" label=" Type of Group(s)/Treatment(s)" help="Type of data in your treatment columns: 'C' for Categorical and 'N' for numerical.  Match the order the groups used. (ie. C,C,N)."/>
+        <param name="interactions" type="boolean" label="Calculate ANOVA with interactions" help="If 'Yes', the ANOVA program will output the interactions."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="results_table" label="${tool.name} on ${on_string}: Results Table"/>
+        <data format="tabular" name="flags_table" label="${tool.name} on ${on_string}: Flags Table"/>
+        <data format="pdf" name="qq_plots" label="${tool.name} on ${on_string}: QQ Plots"/>
+        <data format="pdf" name="volcano_plots" label="${tool.name} on ${on_string}: Volcano Plots"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"       value="ST000006_data.tsv"/>
+            <param name="design"      value="ST000006_design.tsv"/>
+            <param name="uniqID"      value="Retention_Index" />
+            <param name="factor"      value="White_wine_type_and_source" />
+            <param name="factorTypes" value="C" />
+            <output name="results_table" file="ST000006_anova_fixed_with_group_summary.tsv" />
+            <output name="flags_table"   file="ST000006_anova_fixed_with_group_flags.tsv" />
+            <output name="qq_plots"      file="ST000006_anova_fixed_with_group_qq_plots.pdf" compare="sim_size" delta="10000" />
+            <output name="volcano_plots" file="ST000006_anova_fixed_with_group_volcano.pdf"  compare="sim_size" delta="10000" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool fits analysis of variance (ANOVA) fixed effects model with multiple grouping variables, their interactions and numerical characteristics.
+The analysis is performed row wise, independently for each feature.
+The user can choose whether to include interactions between grouping variables in the model or to use a pure additive model.
+Numerical characteristics of the samples can be included for both scenarios.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+
+@WIDE@
+
+**NOTE:** The sample IDs must match the sample IDs in the Design File
+(below). Extra columns will automatically be ignored.
+
+@METADATA@
+
+@UNIQID@
+
+**Group(s)/Treatment(s)**
+
+        - Name of the column(s) (comma separated) in your Design File that you want to use for ANOVA.(ie. treatment1,treatment2,weight).
+
+**Type of Group(s)/Treatment(s)**
+
+        - Type of data in your treatment column(s): 'C' for Categorical and 'N' for numerical. Match the order the groups are used. (ie. C,C,N).
+
+**Calculate ANOVA with interactions**
+
+        - If 'Yes', the ANOVA program will output interactions.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The user will get four different outputs from the fixed effects ANOVA tool:
+
+(1) a TSV file with the results table containing the fixed effects ANOVA results for each variable, the corresponding contrast and analysis of the means.
+(2) a TSV file with the flags for significant p-values.  The flags in the TSV file are equal to 1 if the difference between the groups is statistically significant using the specified α level.
+(3) a PDF file with QQ (quantile-quantile) plots displaying the expected quantiles of a normal distribution on x-axis versus the observed quantiles on y-axis.
+(4) and a Volcano plot with the fold change displayed on the x-axis and the -log 10 of the p-value from the test of the null hypothesis is displayed on the y-axis.  The red dashed line corresponds to p=0.01.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>