--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/standardized_euclidean_distance.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,116 @@
+<tool id="secimtools_standardized_euclidean_distance" name="Standardized Euclidean Distance (SED)" version="@WRAPPER_VERSION@">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+standardized_euclidean_distance.py
+--input $input
+--design $design
+--ID $uniqID
+--fig $plot
+--SEDtoMean $out1
+--SEDpairwise $out2
+
+#if $group
+    --group $group
+#end if
+#if $levels
+	--levels $levels
+#end if
+#if $p
+    --per $p
+#end if
+
+#if $order
+    --order $order
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
+        <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications." />
+        <param name="order" type="text" size="30" label="Input Run Order Name [Optional]" help="Enter the name of the column containing the order samples were run. Spelling and capitalization must be exact." />
+        <param name="levels" type="text" size="30" label="Additional groups to separate by [Optional]" help="Enter additional group(s) name(s). Spelling and capitalization must be exact. If more than one group separate with a ','." />
+        <param name="p" type="float" value= "0.95" size="6" label="Threshold" help="Threshold for standard distribution, specified as percentile. Default = 0.95." />
+    </inputs>
+    <outputs>
+        <data format="pdf" name="plot" label="${tool.name} on ${on_string}: Plot" />
+        <data format="tabular" name="out1" label="${tool.name} on ${on_string}: SEDtoMean" />
+        <data format="tabular" name="out2" label="${tool.name} on ${on_string}: SEDpairwise" />
+    </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" />
+            <output name="plot"  value="ST000006_standardized_euclidean_distance_figure.pdf" compare="sim_size" delta="50000" />
+            <output name="out1"  file="ST000006_standardized_euclidean_distance_to_mean.tsv" />
+            <output name="out2"  file="ST000006_standardized_euclidean_distance_pairwise.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool is designed to identify samples that are different using the standardized Euclidian distance (SED) between samples.
+The tool estimates the variance of features and calculates the SED between each pair of samples in addition to the SED between each sample and the estimated mean.
+If a group or treatment variable is provided, then the same distance plots are generated for each group and for all samples together.
+
+**NOTE:** Groups with less than three samples will be excluded from the analysis.
+
+
+
+**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_OPTIONAL@
+
+    - **Warning:** All groups must contain 3 or more samples.
+
+
+@RUNORDER_OPTIONAL@
+
+**Additional groups to separate by [Optional]**
+
+    - Enter group(s) name(s). Spelling and capitalization must be exact. If more than one group, separate with commas.
+    - **Warning:** All groups must contain 3 or more samples.
+    - **NOTE:** Groups with one element will be excluded from the analysis.
+
+
+**Percentile cutoff**
+
+- The percentile cutoff for standard distributions. The default is 0.95.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool outputs three different files:
+
+(1) a TSV file that contains a n x n matrix (where n is the number computed samples) of the pairwise distances between the samples.
+If the Group/Treatment [Optional] variable is specified, the distances will be computed within groups.
+
+(2) A PDF file containing:
+(i) Boxplots of the distribution of distances.  The distances are computed between samples in the group and summarized as boxplots.
+The outliers (blue dots), means (red squares) and median (blue bars) of the distances are presented for each sample within the group.
+(ii) 2D scatter plots that show distances computed pairwise within the group
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>