--- a/cut.xml	Sat Oct 08 21:01:33 2022 +0000
+++ b/cut.xml	Thu Feb 29 22:15:20 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="tp_cut_tool" name="Advanced Cut" version="@BASE_VERSION@.0">
+<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>columns from a table (cut)</description>
     <macros>
         <import>macros.xml</import>
@@ -8,14 +8,18 @@
     <command>
 <![CDATA[
         cut
-            #if str($delimiter) != '':
-                -d"${delimiter}"
+            $complement
+            $cut_type_options.cut_element
+            #if $cut_type_options.cut_element != '-f'
+                '$cut_type_options.list'
+            #else
+                #if str($cut_type_options.delimiter) != '':
+                    -d"$cut_type_options.delimiter"
+                #end if
+                '$cut_type_options.colnames_option.list'
             #end if
-            ${complement}
-            ${cut_type_options.cut_element}
-            '${cut_type_options.list}'
-            '${input}'
-        > '${output}'
+            '$input'
+        > '$output'
 ]]>
     </command>
     <inputs>
@@ -24,23 +28,33 @@
             <option value="">Keep</option>
             <option value="--complement">Discard</option>
         </param>
-        <param name="delimiter" type="select" label="Delimited by">
-            <option value="">Tab</option>
-            <option value=" ">Whitespace</option>
-            <option value=".">Dot</option>
-            <option value=",">Comma</option>
-            <option value="-">Dash</option>
-            <option value="_">Underscore</option>
-            <option value="|">Pipe</option>
-        </param>
         <conditional name="cut_type_options">
             <param name="cut_element" type="select" label="Cut by">
                 <option value="-f">fields</option>
                 <option value="-c">characters</option>
-                <option value="-b">bytes</option>
             </param>
             <when value="-f">
-                <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
+                <param name="delimiter" type="select" label="Delimited by">
+                    <option value="">Tab</option>
+                    <option value=" ">Whitespace</option>
+                    <option value=".">Dot</option>
+                    <option value=",">Comma</option>
+                    <option value="-">Dash</option>
+                    <option value="_">Underscore</option>
+                    <option value="|">Pipe</option>
+                </param>
+                <conditional name="colnames_option">
+                    <param name="header" type="select" label="Is there a header for the data's columns ?">
+                        <option value="Y">Yes</option>
+                        <option value="N" selected="true">No</option>
+                    </param>
+                    <when value="Y">
+                        <param name="list" type="data_column" data_ref="input" use_header_names="true" multiple="true" label="List of Fields" help="(-f)" />
+                    </when>
+                    <when value="N">
+                        <param name="list" type="data_column" data_ref="input" multiple="true" label="List of Fields" help="(-f)" />
+                    </when>
+                </conditional>
             </when>
             <when value="-c">
                 <param name="list" type="text" value="" label="List of characters" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
@@ -51,15 +65,6 @@
                     </sanitizer>
                 </param>
             </when>
-            <when value="-b">
-                <param name="list" type="text" value="" label="List of Bytes" help="These will be kept/discarded (depending on 'operation'). &lt;BR /&gt; Examples: 1,3,4 or 2-5">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                            <remove value="&apos;"/>
-                        </valid>
-                    </sanitizer>
-                </param>
-            </when>
         </conditional>
     </inputs>
     <outputs>
@@ -70,7 +75,7 @@
                 <conditional name="cut_type_options.cut_element">
                     <!-- fields -->
                     <when value="-f">
-                        <conditional name="delimiter">
+                        <conditional name="cut_type_options.delimiter">
                         <when value="T">
                             <conditional name="input">
                                 <when datatype_isinstance="interval">
@@ -184,20 +189,26 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
             <param name="list" value="1,3,4"/>
             <param name="delimiter" value=""/>
             <output name="output" file="cut_results1.txt"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
-            <param name="list" value="2" />
-            <param name="delimiter" value="" />
+            <conditional name="cut_type_options">
+                <param name="delimiter" value="" />
+                <conditional name="colnames_option">
+                    <param name="header" value="Y"/>
+                    <!-- in the test we can (apparently) not select by header name -->
+                    <param name="list" value="2" />
+                </conditional>
+            </conditional>
             <param name="complement" value="--complement" />
             <output name="output" file="cut_results2.txt"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
             <param name="list" value="-3" />
             <param name="delimiter" value="" />