--- a/SpectraSTSearchAdapter.xml	Thu Dec 01 19:03:12 2022 +0000
+++ b/SpectraSTSearchAdapter.xml	Fri Jun 14 21:34:58 2024 +0000
@@ -1,6 +1,5 @@
-<?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: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Interface to the SEARCH Mode of the SpectraST executable</description>
   <macros>
@@ -17,27 +16,29 @@
 mkdir spectra_files_cond.spectra_files &&
 #if $spectra_files_cond.spectra_files_select == "no"
 mkdir ${' '.join(["'spectra_files_cond.spectra_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && 
-${' '.join(["ln -s '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
+${' '.join(["cp '%s' 'spectra_files_cond.spectra_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 #else
-ln -s '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' &&
+cp '$spectra_files_cond.spectra_files' 'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)' &&
 #end if
 mkdir output_files &&
 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($spectra_files_cond.spectra_files) if f])} && 
 mkdir library_file &&
-ln -s '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
+cp '$library_file' 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)' &&
 #if $sequence_database_file:
   mkdir sequence_database_file &&
-  ln -s '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
+  cp '$sequence_database_file' 'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)' &&
 #end if
 #if $search_file:
   mkdir search_file &&
-  ln -s '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
+  cp '$search_file' 'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)' &&
 #end if
+## advanced options
   #if $adv_opts.user_mod_file:
     mkdir adv_opts.user_mod_file &&
-    ln -s '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
+    cp '$adv_opts.user_mod_file' 'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)' &&
   #end if
 
+
 ## Main program call
 
 set -o pipefail &&
@@ -62,11 +63,13 @@
   -search_file
   'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
 #end if
+## advanced options
   #if $adv_opts.user_mod_file:
     -user_mod_file
     'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
   #end if
 
+
 ## Postprocessing
 ${' '.join(["&& mv -n 'output_files/%(bn)s/%(id)s.%(omsext)s' 'output_files/%(bn)s/%(id)s.%(gext)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
@@ -83,34 +86,34 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
+        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="true" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" multiple="false" optional="false" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
+        <param argument="-spectra_files" type="data" format="dta,mgf,msp,mzdata,mzml,mzxml" label="File names(s) of spectra to be searched" help=" select dta,mgf,msp,mzdata,mzml,mzxml data sets(s)"/>
       </when>
     </conditional>
-    <param name="output_files_type" type="select" optional="false" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
+    <param name="output_files_type" type="select" label="File type of output output_files (Output files. Make sure to specify one output file for each input file)">
       <option value="txt">txt</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="pep.xml">pepxml (pep.xml)</option>
       <option value="pepXML">pepxml</option>
       <option value="html">html</option>
     </param>
-    <param argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
+    <param argument="-library_file" type="data" format="splib" label="Specify library file" help=" select splib data sets(s)"/>
     <param argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
-    <param argument="-sequence_database_type" type="select" optional="true" label="Specify type of sequence database" help="">
+    <param argument="-sequence_database_type" type="select" label="Specify type of sequence database" help="">
       <option value="DNA">DNA</option>
       <option value="AA" selected="true">AA</option>
       <expand macro="list_string_san" name="sequence_database_type"/>
     </param>
     <param argument="-search_file" type="data" format="txt" optional="true" label="Only search a subset of the query spectra in the search file" help=" select txt data sets(s)"/>
-    <param argument="-precursor_mz_tolerance" type="float" optional="true" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
+    <param argument="-precursor_mz_tolerance" type="float" min="0.0" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="Monoisotopic mass is assumed"/>
     <expand macro="adv_opts_macro">
       <param argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
       <param argument="-use_all_charge_states" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Search library spectra of all charge states" help="i.e., ignore specified charge state (if any) of the query spectrum"/>
       <param argument="-user_mod_file" type="data" format="txt" optional="true" label="Specify name of user-defined modifications file" help="Default is &quot;spectrast.usermods&quot; select txt data sets(s)"/>
       <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>
@@ -126,12 +129,13 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_SpectrastSearchAdapter_1 -->
+  <tests>
+    <!-- TOPP_SpectrastSearchAdapter_1 -->
     <!-- TOPP_SpectrastSearchAdapter_2 -->
   </tests>
   <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraSTSearchAdapter.html]]></help>
   <expand macro="references"/>
 </tool>