--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_charges.xml	Mon Jun 05 02:41:30 2023 +0000
@@ -0,0 +1,90 @@
+<tool id="edu.tamu.cpt.tools.charges" name="Charges" version="2.0">
+    <description>colour sequences based on rules</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/fasta_charges.py'
+'$svg'
+@SEQUENCE@
+
+--width '$width'
+
+#if $scheme.cs == "default":
+--aa HSQTNCY AVILMPFWG ERDK
+--fgColor "#000000" "#000000" "#ffffff"
+--bgColor "#ffffff" "#999999" "#000000"
+#elif $scheme.cs == "rb":
+--aa KR ED HSQTNCYAVILMPFWG
+--fgColor "#ffffff" "#ffffff" "#000000"
+--bgColor "#00b0f0" "#fc0000" "#ffffff"
+#elif $scheme.cs == "rbgb":
+--aa KR ED P C HSQTNYAVILMFWG
+--fgColor "#ffffff" "#ffffff" "#ffffff" "#ffffff" "#000000"
+--bgColor "#00b0f0" "#fc0000" "#1cb026" "#805839" "#ffffff"
+#else:
+	--aa
+	#for group in '$scheme.groups':
+		"$group.aminoAcids"
+	#end for
+	--fgColor
+	#for group in '$scheme.groups':
+		"$group.fgColour"
+	#end for
+	--bgColor
+	#for group in '$scheme.groups':
+		"$group.bgColour"
+	#end for
+#end if
+
+> $html ]]>
+</command>
+    <inputs>
+        <expand macro="input/fasta/protein"/>
+        <param label="Output format" name="svg" type="select">
+            <option value="">HTML</option>
+            <option value="--svg">SVG</option>
+        </param>
+        <conditional name="scheme">
+            <param label="Colour scheme" name="cs" type="select">
+                <option value="default">Default hyrophobic/polar/charged</option>
+                <option value="rb">Positives Blue, Negatives Red</option>
+                <option value="rbgb">Positives Blue, Negatives Red, Prolines Green, Cysteines Brown</option>
+                <option value="custom">Custom Colour Scheme</option>
+            </param>
+            <when value="default"/>
+            <when value="rb"/>
+            <when value="custom">
+                <repeat name="groups" title="Colour Group">
+                    <param name="aminoAcids" type="text" label="Amino Acids" help="Amino acids to colour a specific colour"/>
+                    <param name="fgColour" type="color" label="Foreground Color"/>
+                    <param name="bgColour" type="color" label="Background Color"/>
+                </repeat>
+            </when>
+        </conditional>
+        <param label="Plot width" name="width" type="integer" value="120"/>
+    </inputs>
+    <outputs>
+        <data format="html" name="html">
+            <change_format>
+                <when input="svg" value="--svg" format="svg"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequences" value="prot.fa"/>
+            <param name="cs" value="default"/>
+            <param name="width" value="120"/>
+            <output name="html" file="charges.html"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Colors fasta (protein) sequences based on rules, and displays outputs as HTML.
+</help>
+    <expand macro="citations"/>
+</tool>