--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subset_data.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,82 @@
+<tool id="secimtools_subset_data" name="Subset Wide Data and Design File" version="@WRAPPER_VERSION@">
+    <description>- Based on groups.</description>
+    <requirements>
+        <requirement type="python-module">os</requirement>
+        <requirement type="python-module">pandas</requirement>
+        <requirement type="python-module">interface</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        subset_data.py
+        --input $input
+        --design $design
+        --uniqID $uniqID
+        #if $group
+            --group $group
+        #end if
+        --drops $toDrop
+        --out $out
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
+        <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
+        <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s)/Sample(s), comma separated, that will be removed from your wide datset."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
+    </outputs>
+    <macros>
+            <import>macros.xml</import>
+    </macros>
+    <tests>
+     <test>
+        <param name="input"  value="ST000006_data.tsv"/>
+        <param name="design" value="ST000006_design_names_underscore.tsv"/>
+        <param name="uniqID" value="Retention_Index" />
+        <param name="group"  value="White_wine_type_and_source" />
+        <param name="drops"  value="Chardonnay_ Napa_ CA 2003,Riesling_ CA 2004" />
+        <output name="out"   file="ST000006_subset_data_output.tsv" />
+     </test>
+    </tests>
+<help>
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool creates new wide format dataset and design dataset based on the existing wide and design datasets where only groups specified by the user are present.  
+The user chooses which group(s) to include in the new datasets.
+
+--------------------------------------------------------------------------------
+
+**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 in your Design File that contains group classifications. If none provided the drop will be performed by 'sampleID'.
+
+**Group(s)/Sample(s) to drop**
+
+    - Name of the Group(s)/Sample(s), comma separeted, that will be removed from your wide datset.
+    
+--------------------------------------------------------------------------------
+
+**Output**
+
+This tool will output two TSV files: a TSV file containing the subset of the original wide format dataset and a TSV file containing the subset of the original design dataset.  Both datasets will contain only the samples belonging to groups selected by the user.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>