--- a/IDMassAccuracy.xml	Fri Nov 06 20:39:42 2020 +0000
+++ b/IDMassAccuracy.xml	Thu Dec 01 18:58:59 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="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
   <macros>
     <token name="@EXECUTABLE@">IDMassAccuracy</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -16,10 +14,20 @@
 #import re
 
 ## Preprocessing
-mkdir in &&
-${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
-mkdir id_in &&
-${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
+mkdir in_cond.in &&
+#if $in_cond.in_select == "no"
+mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
+${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+#end if
+mkdir id_in_cond.id_in &&
+#if $id_in_cond.id_in_select == "no"
+mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} && 
+${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
+#else
+ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
+#end if
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_precursor &&
 #end if
@@ -40,9 +48,17 @@
 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
-${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+#if $in_cond.in_select == "no"
+${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+#else
+'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
+#end if
 -id_in
-${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
+#if $id_in_cond.id_in_select == "no"
+${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
+#else
+'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
+#end if
 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_precursor
   'out_precursor/output.${gxy2omsext("tabular")}'
@@ -84,16 +100,38 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
-    <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
-    <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
-    <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
-    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
+    <conditional name="in_cond">
+      <param name="in_select" type="select" label="Run tool in batch mode for -in">
+        <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="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+      </when>
+    </conditional>
+    <conditional name="id_in_cond">
+      <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
+        <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="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+      </when>
+      <when value="yes">
+        <param argument="-id_in" type="data" format="idxml" multiple="false" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+      </when>
+    </conditional>
+    <param argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
+    <param argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
+    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
     <expand macro="adv_opts_macro">
-      <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
-      <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="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
+      <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">
@@ -124,13 +162,37 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_IDMassAccuracy"/>
-    <expand macro="manutest_IDMassAccuracy"/>
+  <tests><!-- TOPP_IDMassAccuracy_1 -->
+    <test expect_num_outputs="5">
+      <section name="adv_opts">
+        <param name="number_of_bins" value="10"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <conditional name="in_cond">
+        <param name="in" value="spectra.mzML"/>
+      </conditional>
+      <conditional name="id_in_cond">
+        <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
+      </conditional>
+      <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <param name="precursor_error_ppm" value="false"/>
+      <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <param name="fragment_error_ppm" value="false"/>
+      <param name="fragment_mass_tolerance" value="0.5"/>
+      <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDMassAccuracy.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDMassAccuracy.html]]></help>
   <expand macro="references"/>
 </tool>