--- a/RNADigestor.xml	Thu Dec 01 19:19:16 2022 +0000
+++ b/RNADigestor.xml	Fri Jun 14 21:46:15 2024 +0000
@@ -1,8 +1,7 @@
-<?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
-<!--Proposed Tool Section: [Utilities]-->
+<!--Proposed Tool Section: [RNA]-->
 <tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Digests an RNA sequence database in-silico.</description>
+  <description>Digests an RNA sequence database in-silico</description>
   <macros>
     <token name="@EXECUTABLE@">RNADigestor</token>
     <import>macros.xml</import>
@@ -15,7 +14,7 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,19 +38,19 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="fasta" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
-    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
-    <param argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/>
-    <param argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/>
-    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme (RNase)" help="">
-      <option value="RNase_U2">RNase_U2</option>
-      <option value="RNase_A">RNase_A</option>
-      <option value="RNase_MC1">RNase_MC1</option>
+    <param argument="-in" type="data" format="fasta" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
+    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
+    <param argument="-min_length" type="integer" value="3" label="Minimum length of a fragment" help=""/>
+    <param argument="-max_length" type="integer" value="30" label="Maximum length of a fragment" help=""/>
+    <param argument="-enzyme" type="select" label="Digestion enzyme (RNase)" help="">
+      <option value="RNase_T1" selected="true">RNase_T1</option>
       <option value="RNase_H">RNase_H</option>
-      <option value="cusativin">cusativin</option>
-      <option value="RNase_T1" selected="true">RNase_T1</option>
       <option value="mazF">mazF</option>
       <option value="colicin_E5">colicin_E5</option>
+      <option value="RNase_MC1">RNase_MC1</option>
+      <option value="RNase_A">RNase_A</option>
+      <option value="RNase_U2">RNase_U2</option>
+      <option value="cusativin">cusativin</option>
       <option value="no cleavage">no cleavage</option>
       <option value="unspecific cleavage">unspecific cleavage</option>
       <expand macro="list_string_san" name="enzyme"/>
@@ -60,7 +59,7 @@
     <param argument="-cdna" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Input file contains cDNA sequences - replace 'T' with 'U')" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -74,15 +73,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--random RNAsequence input -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="fasta" value="random_RNA.fa"/>
-    <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--random RNAsequence input -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="fasta" value="random_RNA.fa"/>
+      <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
+    </test>
+  </tests>
   <help><![CDATA[Digests an RNA sequence database in-silico.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNADigestor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNADigestor.html]]></help>
   <expand macro="references"/>
 </tool>