--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ttest_single_group.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,100 @@
+<tool id="secimtools_ttest_single_group" name="T-Test (Single Group)" version="@WRAPPER_VERSION@">
+    <description>for the specified mean.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+ttest_single_group.py
+--input $input
+--design $design
+--uniqueID $uniqueID
+--mu $mu
+--summaries $summaries
+--flags $flags
+--volcano $volcano
+#if $group
+    --group $group
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
+        <param name="mu" type="text" size="30" value = "0" label="Mu" help="The value of the mean under the null hypothesis. Default = 0. "/>
+        <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
+        <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01, 0.05 and 0.10 significance levels for the differences. "/>
+        <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"      value="ST000006_data.tsv"/>
+            <param name="design"     value="ST000006_design.tsv"/>
+            <param name="uniqueID"   value="Retention_Index" />
+            <param name="mu"         value="0" />
+            <output name="summaries" file="ST000006_ttest_single_group_no_group_summary.tsv" />
+            <output name="flags"     file="ST000006_ttest_single_group_no_group_flags.tsv" />
+            <output name="volcano"   file="ST000006_ttest_single_group_no_group_volcano.pdf" compare="sim_size" delta="10000"/>
+        </test>
+        <test>
+            <param name="input"       value="ST000006_data.tsv"/>
+            <param name="design"      value="ST000006_design.tsv"/>
+            <param name="uniqueID"    value="Retention_Index" />
+            <param name="mu"          value="0" />
+            <param name="group"       value="White_wine_type_and_source" />
+            <output name="summaries"  file="ST000006_ttest_single_group_with_group_summary.tsv" />
+            <output name="flags"      file="ST000006_ttest_single_group_with_group_flags.tsv" />
+            <output name="volcano"    file="ST000006_ttest_single_group_with_group_volcano.pdf" compare="sim_size" delta="10000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool performs a one sample t-test for each feature.
+Two options are available for the t-test: if the user provides the Group/Treatment variable, then the mean for each treatment condition is compared with Mu, the user-specified value of the true mean under the null hypothesis.
+If Group/Treatment is not provided, then the mean across all samples is compared to Mu.
+
+--------------------------------------------------------------------------------
+
+**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/Treatment [Optional]**
+
+        - Name of the column the Design File that contains group classifications.
+
+**Mu**
+
+        - The value of the mean under the null hypothesis. Default = 0.
+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool produces three outputs:
+
+(1)  a TSV file with the results table containing p-values for each test and the corresponding differences between the group means and the mu value under the null.
+(2) a TSV file containing indicator flags equal to 1 if the difference between the groups and the mean under the null is statistically significant using the indicated α levels.
+(3) a PDF file with volcano plots for visual inspection of the differences between the group means and p-values. The red dashed line in the volcano plot(s) corresponds to a p-value = 0.01 cutoff (2 on the negative log base 10 scale).
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>