--- a/SpectraSTSearchAdapter.xml	Fri Nov 06 20:14:43 2020 +0000
+++ b/SpectraSTSearchAdapter.xml	Thu Dec 01 19:03:12 2022 +0000
@@ -1,13 +1,11 @@
 <?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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<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>
     <token name="@EXECUTABLE@">SpectraSTSearchAdapter</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,9 +14,15 @@
 #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 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])}
+#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)' &&
+#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)' &&
 #if $sequence_database_file:
@@ -29,12 +33,10 @@
   mkdir search_file &&
   ln -s '$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)' &&
+  #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)' &&
   #end if
-#end if
 
 ## Main program call
 
@@ -43,9 +45,13 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -spectra_files
-${' '.join(["'spectra_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $spectra_files if _])}
+#if $spectra_files_cond.spectra_files_select == "no"
+${' '.join(["'spectra_files_cond.spectra_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
+#else
+'spectra_files_cond.spectra_files/${re.sub("[^\w\-_]", "_", $spectra_files_cond.spectra_files.element_identifier)}.$gxy2omsext($spectra_files_cond.spectra_files.ext)'
+#end if
 -output_files
-${' '.join(["'output_files/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $output_files_type) for _ in $spectra_files if _])}
+${' '.join(["'output_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $output_files_type) for i, f in enumerate($spectra_files_cond.spectra_files) if f])}
 -library_file
 'library_file/${re.sub("[^\w\-_]", "_", $library_file.element_identifier)}.$gxy2omsext($library_file.ext)'
 #if $sequence_database_file:
@@ -56,15 +62,13 @@
   -search_file
   'search_file/${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:
+  #if $adv_opts.user_mod_file:
     -user_mod_file
-    'adv_opts_cond.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts_cond.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts_cond.user_mod_file.ext)'
+    'adv_opts.user_mod_file/${re.sub("[^\w\-_]", "_", $adv_opts.user_mod_file.element_identifier)}.$gxy2omsext($adv_opts.user_mod_file.ext)'
   #end if
-#end if
 
 ## 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 $spectra_files if _])}
+${' '.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 $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -73,7 +77,18 @@
     <configfile name="hardcoded_json"><![CDATA[{"executable": "spectrast", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="spectra_files" 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)"/>
+    <conditional name="spectra_files_cond">
+      <param name="spectra_files_select" type="select" label="Run tool in batch mode for -spectra_files">
+        <option value="no">No: process all datasets jointly</option>
+        <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)"/>
+      </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)"/>
+      </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)">
       <option value="txt">txt</option>
       <option value="tsv">tabular (tsv)</option>
@@ -81,22 +96,22 @@
       <option value="pepXML">pepxml</option>
       <option value="html">html</option>
     </param>
-    <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="">
+    <param argument="-library_file" type="data" format="splib" optional="false" 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="">
       <option value="DNA">DNA</option>
       <option value="AA" selected="true">AA</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="sequence_database_type"/>
     </param>
-    <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"/>
+    <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"/>
     <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="Overrides 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 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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -105,19 +120,18 @@
   </inputs>
   <outputs>
     <collection type="list" name="output_files" label="${tool.name} on ${on_string}: output_files">
-      <discover_datasets directory="output_files" pattern="__name_and_ext__"/>
+      <discover_datasets directory="output_files" recurse="true" pattern="__name_and_ext__"/>
     </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SpectraSTSearchAdapter"/>
-    <expand macro="manutest_SpectraSTSearchAdapter"/>
+  <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/2.6.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SpectraSTSearchAdapter.html]]></help>
   <expand macro="references"/>
 </tool>