--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_flags.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,70 @@
+<tool id="secimtools_summarize_flags" name="Summarize Flags in a Flag File" version="@WRAPPER_VERSION@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+summarize_flags.py
+--flags $flags
+--ID $uniqID
+--outSummary $summaryFlags
+    ]]></command>
+    <inputs>
+        <param name="flags" type="data" format="tabular" label="Flag File"
+               help="Input dataset containing the binary indicator flag values for each feature."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID"
+               help="Name of the column in your flag file containing  unique identifiers."/>
+    </inputs>
+    <outputs>
+        <data name="summaryFlags" format="tabular" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="flags"   value="ST000006_lasso_enet_var_select_flags.tsv"/>
+            <param name="uniqID"  value="Retention_Index" />
+            <output name="summaryFlags" file="ST000006_summarize_flags_outSummary.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+Summary of the Flags
+
+This tool takes a wide format flag file and summarizes information about the flags.
+The flag summary includes, for each feature:
+(i) the sum of the flags,
+(ii) the mean of the flags,
+(iii) an indicator if at least one of the original flags had a value of 1 and
+(iv) a second indicator if all of the original flags had a value of 1.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - One input dataset is required.
+
+@FLAGS@
+
+@UNIQID@
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+This tool will output a TSV file containing all original input flag data with four additional columns containing the flag summaries.
+
+The four additional columns are:
+
+(i) a column with the sum of the flags,
+(ii) a column with the flag means, and
+(iii) a flag indicator column if at least one of the original flags had a value of 1
+(iv) a second flag indicator column if all of the original flags had a value of 1
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>