--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wig_rebase.xml	Mon Jun 05 02:54:16 2023 +0000
@@ -0,0 +1,59 @@
+<tool id="edu.tamu.cpt.wig.rebase" name="Rebase Wig Analysis Results" version="19.1.0.0">
+  <description>against parent features</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>cpt-macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/wig_rebase.py'
+'$parent'
+'$wigFile'
+
+'$protein2dna'
+--map_by "$map_by"
+> '$output']]></command>
+  <inputs>
+    <param label="Parent GFF3 annotations" name="parent" format="gff3" type="data"/>
+    <param label="Wig Results" name="wigFile" format="wig" type="data"/>
+    <param label="Map protein translated results to original DNA data" name="protein2dna" type="boolean" truevalue="--protein2dna" falsevalue=""/>
+    <param label="Mapping Key" name="map_by" type="text" value="ID"/>
+  </inputs>
+  <outputs>
+    <data format="wig" name="output"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="parent" value="T7_CLEAN.gff3"/>
+      <param name="wigFile" value="T7_BW_I.wig"/>
+      <param name="protein2dna" value="--protein2dna"/>
+      <param name="map_by" value="ID"/>
+      <output name="output" file="T7_BW_I_REBASE.wig"/>
+    </test>
+    <test>
+      <param name="parent" value="tmhmm.parent.gff3"/>
+      <param name="wigFile" value="tmhmm_m.wig"/>
+      <param name="protein2dna" value="--protein2dna"/>
+      <param name="map_by" value="ID"/>
+      <output name="output" file="rebased_m.wig"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Rebases wig results against a set of gff3 annotations which were involved in producing that data.
+
+For example, imagine you take a gff3 file, and export the CDS sequences in
+order to analyse in TMHMM. Having done this, you want to view the associated
+Wig files in JBrowse with your TMHMM results. This tool will re-map the wig
+data to the correct location in the parent genome.
+
+E.g. Given
+
+-  A feature (gp01) runs from 2000-2200
+-  A wig file with data from 1-200
+
+The data would be re-mapped and you would receive a wig file with data from 2000-2200.
+]]></help>
+  <expand macro="citations"/>
+</tool>