--- a/SpectraSTSearchAdapter.xml	Fri May 17 10:13:17 2019 -0400
+++ b/SpectraSTSearchAdapter.xml	Wed Sep 09 12:53:13 2020 +0000
@@ -1,100 +1,124 @@
 <?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]-->
-<tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="2.3.0">
+<tool id="SpectraSTSearchAdapter" name="SpectraSTSearchAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Interface to the SEARCH Mode of the SpectraST executable</description>
   <macros>
     <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[SpectraSTSearchAdapter
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
+## Preprocessing
+mkdir spectra_files &&
+${ ' '.join(["ln -s '%s' 'spectra_files/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _]) }
+mkdir output_files &&
+mkdir library_file &&
+ln -s '$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)' &&
+#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)' &&
+#end if
+#if $adv_opts_cond.adv_opts_selector=='advanced':
+  #if $adv_opts_cond.user_mod_file:
+    mkdir adv_opts_cond.user_mod_file &&
+    ln -s '$adv_opts_cond.user_mod_file' 'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)' &&
+  #end if
+#end if
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -spectra_files
-  #for token in $param_spectra_files:
-    $token
-  #end for
-
-#if $rep_param_output_files:
+${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
 -output_files
-  #for token in $rep_param_output_files:
-    #if " " in str(token):
-      "$token.param_output_files"
-    #else
-      $token.param_output_files
-    #end if
-  #end for
+${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
+-library_file
+'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
+#if $sequence_database_file:
+  -sequence_database_file
+  'sequence_database_file/${re.sub("[^\w\-_]", "_", $sequence_database_file.element_identifier)}.$gxy2omsext($sequence_database_file.ext)'
 #end if
-#if $param_library_file:
-  -library_file $param_library_file
-#end if
-#if $param_sequence_database_file:
-  -sequence_database_file $param_sequence_database_file
+#if $search_file:
+  -search_file
+  'search_file/${re.sub("[^\w\-_]", "_", $search_file.element_identifier)}.$gxy2omsext($search_file.ext)'
 #end if
-#if $param_sequence_database_type:
-  -sequence_database_type
-  #if " " in str($param_sequence_database_type):
-    "$param_sequence_database_type"
-  #else
-    $param_sequence_database_type
+#if $adv_opts_cond.adv_opts_selector=='advanced':
+  #if $adv_opts_cond.user_mod_file:
+    -user_mod_file
+    'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)'
   #end if
 #end if
-#if $param_search_file:
-  -search_file $param_search_file
-#end if
-#if $param_params_file:
-  -params_file $param_params_file
-#end if
-#if $param_precursor_mz_tolerance:
-  -precursor_mz_tolerance $param_precursor_mz_tolerance
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_use_isotopically_averaged_mass:
-  -use_isotopically_averaged_mass
-#end if
-    #if $adv_opts.param_use_all_charge_states:
-  -use_all_charge_states
-#end if
-    #if $adv_opts.param_user_mod_file:
-  -user_mod_file $adv_opts.param_user_mod_file
-#end if
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+
+## Postprocessing
+${' '.join(["&& mv -n 'output_files/%(id)s.%(omsext)s' 'output_files/%(id)s.%(gext)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "omsext":$output_files_type, "gext": $oms2gxyext(str($output_files_type))} for _ in $spectra_files if _])}
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_spectra_files" type="data" format="mzml,mzxml,mzData,dta,msp" multiple="true" optional="False" size="30" label="File names(s) of spectra to be searched" help="(-spectra_files) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="spectra_files" argument="-spectra_files" type="data" format="dta,msp,mzdata,mzml,mzxml" multiple="true" optional="false" label="File names(s) of spectra to be searched" help=" select dta,msp,mzdata,mzml,mzxml data sets(s)"/>
+    <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)">
+      <option value="txt">txt</option>
+      <option value="tsv">tabular (tsv)</option>
+      <option value="pep.xml">pepxml (pep.xml)</option>
+      <option value="xml">xml</option>
+      <option value="pepXML">pepxml</option>
+      <option value="html">html</option>
     </param>
-    <param name="param_library_file" type="data" format="splib" optional="False" label="Specify library file" help="(-library_file) "/>
-    <param name="param_sequence_database_file" type="data" format="fasta" optional="True" label="The sequence database" help="(-sequence_database_file) "/>
-    <param name="param_sequence_database_type" display="radio" type="select" optional="False" value="AA" label="Specify type of sequence database" help="(-sequence_database_type) ">
+    <param name="library_file" argument="-library_file" type="data" format="splib" optional="false" label="Specify library file" help=" select splib data sets(s)"/>
+    <param name="sequence_database_file" argument="-sequence_database_file" type="data" format="fasta" optional="true" label="The sequence database" help=" select fasta data sets(s)"/>
+    <param name="sequence_database_type" argument="-sequence_database_type" display="radio" type="select" optional="false" label="Specify type of sequence database" help="">
       <option value="DNA">DNA</option>
       <option value="AA" selected="true">AA</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_search_file" type="data" format="txt,dat" optional="True" label="Only search a subset of the query spectra in the search file" help="(-search_file) "/>
-    <param name="param_params_file" type="data" format="params" optional="True" label="Read search options from file" help="(-params_file) All options set in the file will be overridden by command-line options, if specified"/>
-    <param name="param_precursor_mz_tolerance" type="float" min="0.0" optional="True" value="3.0" label="m/z (in Th) tolerance within which candidate entries are compared to the query" help="(-precursor_mz_tolerance) Monoisotopic mass is assumed"/>
-    <expand macro="advanced_options">
-      <param name="param_use_isotopically_averaged_mass" display="radio" type="boolean" truevalue="-use_isotopically_averaged_mass" falsevalue="" checked="false" optional="True" label="Use isotopically averaged mass instead of monoisotopic mass" help="(-use_isotopically_averaged_mass) "/>
-      <param name="param_use_all_charge_states" display="radio" type="boolean" truevalue="-use_all_charge_states" falsevalue="" checked="false" optional="True" label="Search library spectra of all charge states, i.e., ignore specified charge state (if any) of the query spectrum" help="(-use_all_charge_states) "/>
-      <param name="param_user_mod_file" type="data" format="txt" label="Specify name of user-defined modifications file" help="(-user_mod_file) Default is &quot;spectrast.usermods&quot;"/>
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="search_file" 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 name="precursor_mz_tolerance" 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"/>
+    <expand macro="adv_opts_macro">
+      <param name="use_isotopically_averaged_mass" argument="-use_isotopically_averaged_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use isotopically averaged mass instead of monoisotopic mass" help=""/>
+      <param name="use_all_charge_states" 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 name="user_mod_file" 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 name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san"/>
+      </param>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_output_files" format="txt"/>
+    <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
+      <discover_datasets directory="output_files" pattern="__name_and_ext__"/>
+    </collection>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Interface to the SEARCH Mode of the SpectraST executable
+  <tests>
+    <expand macro="autotest_SpectraSTSearchAdapter"/>
+    <expand macro="manutest_SpectraSTSearchAdapter"/>
+  </tests>
+  <help><![CDATA[Interface to the SEARCH Mode of the SpectraST executable
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_SpectraSTSearchAdapter.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_SpectraSTSearchAdapter.html]]></help>
+  <expand macro="references"/>
 </tool>