--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_design_file.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,77 @@
+<tool id="secimtools_modify_design_file" name="Modify design file" version="@WRAPPER_VERSION@">
+    <description>to remove specified group types or sampleIDs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+modify_design_file.py
+--input $input
+--design $design
+--uniqID $uniqID
+#if $group
+    --group $group
+#end if
+--drops $toDrop
+--out $out
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
+        <param name="group" type="text" size="30" value="" optional="false" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classifications. If not provided, the drop will be performed by 'sampleID'."/>
+        <param name="toDrop" type="text" size="30" optional="false" label="Group(s)/Sample(s) to drop" help="Name of the Group(s) or Sample(s), comma separated, to remove from your design file."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Value"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"  value="ST000006_data.tsv"/>
+            <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
+            <param name="uniqID" value="Retention_Index" />
+            <param name="group"  value="White_wine_type_and_source_no_space" />
+            <param name="toDrop" value="Chardonnay_Napa_CA2003,Riesling_CA2004,SauvignonBlanc_LakeCounty_CA2001" />
+            <output name="out"   file="ST000006_modify_design_output.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool creates a new design file based on the existing wide dataset and design file where the specified group types or samples are removed from the existing design file.
+
+--------------------------------------------------------------------------------
+
+**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 not provided, the drop will be performed by 'sampleID's.
+
+**Group(s)/Sample(s) to drop**
+
+    - Name of the Group(s) or Sample(s), comma separated, to remove from the design file.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+This tool will output a single design file that contains only the samples not selected for removal.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>