--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_rank_wide.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,55 @@
+<tool id="secimtools_generate_rank_wide" name="Ranked wide file"  version="@WRAPPER_VERSION@">
+    <description>Generate a wide format file with ranked columns from an input wide file.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+addGroupRank.py
+--wide $wide
+--design $design
+--out $out
+#if $ngroup:
+    --ngroup $ngroup
+#end if
+--rank $rank
+--uniqID $uniqID
+    ]]></command>
+    <inputs>
+        <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
+        <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/>
+        <param name="rank" type="text" size="30" value="Rank" label=" Name of flag column" help="The column name in your design file that contains the flags to specify whether a sampleID will be ranked in the input wide file."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/>
+    </outputs>
+
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+The tool is used to generate a wide format file with each column being ranked in the input wide format dataset.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The user will get a output file from the tool:
+
+(1) a wide format file with each column being ranked. The columns will be selected using the flag column in the design file.
+
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>