--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/secimtools/threshold_based_flags.xml	Mon Mar 08 20:55:03 2021 +0000
@@ -0,0 +1,78 @@
+<tool id="secimtools_threshold_based_flags" name="Threshold Based Flags" version="@WRAPPER_VERSION@">
+    <description>to flag features based on a user-specified threshold.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+threshold_based_flags.py
+--input $input
+--design $design
+--ID $uniqID
+--output $output
+--group $group
+
+#if $cutoff:
+--cutoff $cutoff
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
+        <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications.  The resulting indicator flags will generated for these group categories." />
+        <param name="cutoff" type="integer" optional="true" size="6" value="30000" label="Cutoff" help="Cutoff to use for which values to flag. Defaults = 30,000."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+    </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="group"   value="White_wine_type_and_source" />
+            <param name="cutoff"  value="3000" />
+            <output name="output" file="ST000006_threshold_based_flags_output.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+This tool flags a feature in a given group with a binary indicator if, for half (or more) of the samples within the group, the feature value is below a user specified threshold or is missing.
+The default threshold value of 30,000 is primarily useful for peak intensities from mass spectroscopy data and should be evaluated carefully for other types of values (e.g. for peak height).
+
+--------------------------------------------------------------------------------
+
+
+**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@
+
+**Cutoff Value**
+
+    - Cutoff to use for which values to flag. Default = 30,000.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+This tool outputs a TSV file containing indicator flags for each group, where the number of indicator flags is determined by the number of groups.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>