--- a/MassCalculator.xml	Fri May 17 09:47:58 2019 -0400
+++ b/MassCalculator.xml	Wed Sep 09 12:46:33 2020 +0000
@@ -1,103 +1,76 @@
 <?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="MassCalculator" name="MassCalculator" version="2.3.0">
+<tool id="MassCalculator" name="MassCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
   <macros>
     <token name="@EXECUTABLE@">MassCalculator</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
-  <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[MassCalculator
-
-#if $param_in:
-  -in $param_in
-#end if
+  <expand macro="stdio"/>
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $rep_param_in_seq:
--in_seq
-  #for token in $rep_param_in_seq:
-    #if " " in str(token):
-      "$token.param_in_seq"
-    #else
-      $token.param_in_seq
-    #end if
-  #end for
+## Preprocessing
+#if $in:
+  mkdir in &&
+  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
-#if $param_out:
-  -out $param_out
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out &&
 #end if
 
-#if $rep_param_charge:
--charge
-  #for token in $rep_param_charge:
-    #if " " in str(token):
-      "$token.param_charge"
-    #else
-      $token.param_charge
-    #end if
-  #end for
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+#if $in:
+  -in
+  'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 #end if
-#if $param_format:
-  -format
-  #if " " in str($param_format):
-    "$param_format"
-  #else
-    $param_format
-  #end if
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out
+  'out/output.${gxy2omsext("txt")}'
 #end if
-#if $param_average_mass:
-  -average_mass
-#end if
-#if $param_fragment_type:
-  -fragment_type
-  #if " " in str($param_fragment_type):
-    "$param_fragment_type"
-  #else
-    $param_fragment_type
-  #end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
 #end if
-#if $param_separator:
-  -separator     "$param_separator"
+
+## Postprocessing
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out/output.${gxy2omsext("txt")}' '$out'
 #end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+#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[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in) "/>
-    <repeat name="rep_param_in_seq" min="0" title="param_in_seq">
-      <param name="param_in_seq" type="text" size="30" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq) ">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
-    </repeat>
-    <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
-      <param name="param_charge" type="text" size="30" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge) ">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
-    </repeat>
-    <param name="param_format" display="radio" type="select" optional="False" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="(-format) ">
+    <param name="in" argument="-in" type="data" format="txt" optional="true" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help=" select txt data sets(s)"/>
+    <param name="in_seq" argument="-in_seq" type="text" optional="true" value="" label="List of peptide sequences (mutually exclusive to 'in')" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_string_val"/>
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="charge" argument="-charge" type="text" optional="true" value="0" label="List of charge states; required if 'in_seq' is given" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+      <expand macro="list_integer_valsan"/>
+    </param>
+    <param name="format" argument="-format" display="radio" type="select" optional="false" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="">
       <option value="list" selected="true">list</option>
       <option value="table">table</option>
       <option value="mass_only">mass_only</option>
       <option value="mz_only">mz_only</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_average_mass" display="radio" type="boolean" truevalue="-average_mass" falsevalue="" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass) "/>
-    <param name="param_fragment_type" type="select" optional="False" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) ">
+    <param name="average_mass" argument="-average_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Compute average (instead of monoisotopic) peptide masses" help=""/>
+    <param name="fragment_type" argument="-fragment_type" type="select" optional="false" label="For what type of sequence/fragment the mass should be computed" help="">
       <option value="full" selected="true">full</option>
       <option value="internal">internal</option>
       <option value="N-terminal">N-terminal</option>
@@ -108,24 +81,40 @@
       <option value="x-ion">x-ion</option>
       <option value="y-ion">y-ion</option>
       <option value="z-ion">z-ion</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_separator" type="text" size="30" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="separator" argument="-separator" type="text" optional="true" value="" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="">
+      <expand macro="list_string_san"/>
     </param>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <expand macro="adv_opts_macro">
+      <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="false">
+      <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="txt"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="txt">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Calculates masses and mass-to-charge ratios of peptide sequences
+  <tests>
+    <expand macro="autotest_MassCalculator"/>
+    <expand macro="manutest_MassCalculator"/>
+  </tests>
+  <help><![CDATA[Calculates masses and mass-to-charge ratios of peptide sequences
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MassCalculator.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_MassCalculator.html]]></help>
+  <expand macro="references"/>
 </tool>