--- a/Digestor.xml	Fri May 17 10:20:34 2019 -0400
+++ b/Digestor.xml	Thu Sep 03 16:23:17 2020 +0000
@@ -1,99 +1,132 @@
 <?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="Digestor" name="Digestor" version="2.3.0">
+<tool id="Digestor" name="Digestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Digests a protein database in-silico.</description>
   <macros>
     <token name="@EXECUTABLE@">Digestor</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[Digestor
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${out_type}'
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_out_type:
-  -out_type
-  #if " " in str($param_out_type):
-    "$param_out_type"
-  #else
-    $param_out_type
-  #end if
-#end if
-#if $param_missed_cleavages:
-  -missed_cleavages $param_missed_cleavages
-#end if
-#if $param_min_length:
-  -min_length $param_min_length
-#end if
-#if $param_max_length:
-  -max_length $param_max_length
-#end if
-#if $param_enzyme:
-  -enzyme
-  #if " " in str($param_enzyme):
-    "$param_enzyme"
-  #else
-    $param_enzyme
-  #end if
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${out_type}' '$out'
+#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="fasta" optional="False" label="input file" help="(-in) "/>
-    <param name="param_out_type" display="radio" type="select" optional="True" label="Set this if you cannot control the filename of 'out'," help="(-out_type) e.g., in TOPPAS">
-      <option value="idXML">idXML</option>
+    <param name="in" argument="-in" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/>
+    <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Set this if you cannot control the filename of 'out'" help="e.g., in TOPPAS">
       <option value="fasta">fasta</option>
+      <option value="idXML">idxml</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="The number of allowed missed cleavages" help="(-missed_cleavages) "/>
-    <param name="param_min_length" type="integer" value="6" label="Minimum length of peptide" help="(-min_length) "/>
-    <param name="param_max_length" type="integer" value="40" label="Maximum length of peptide" help="(-max_length) "/>
-    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The type of digestion enzyme" help="(-enzyme) ">
+    <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
+    <param name="min_length" argument="-min_length" type="integer" optional="true" value="6" label="Minimum length of peptide" help=""/>
+    <param name="max_length" argument="-max_length" type="integer" optional="true" value="40" label="Maximum length of peptide" help=""/>
+    <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The type of digestion enzyme" help="">
+      <option value="Asp-N">Asp-N</option>
+      <option value="Asp-N/B">Asp-N/B</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="cyanogen-bromide">cyanogen-bromide</option>
+      <option value="Clostripain/P">Clostripain/P</option>
+      <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="staphylococcal protease/D">staphylococcal protease/D</option>
+      <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
+      <option value="Glu-C+P">Glu-C+P</option>
+      <option value="PepsinA + P">PepsinA + P</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
       <option value="proline endopeptidase">proline endopeptidase</option>
-      <option value="V8-DE">V8-DE</option>
-      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
-      <option value="no cleavage">no cleavage</option>
-      <option value="2-iodobenzoate">2-iodobenzoate</option>
-      <option value="leukocyte elastase">leukocyte elastase</option>
-      <option value="V8-E">V8-E</option>
-      <option value="unspecific cleavage">unspecific cleavage</option>
-      <option value="Arg-C">Arg-C</option>
-      <option value="CNBr">CNBr</option>
-      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
       <option value="Chymotrypsin">Chymotrypsin</option>
       <option value="Chymotrypsin/P">Chymotrypsin/P</option>
-      <option value="TrypChymo">TrypChymo</option>
-      <option value="Asp-N_ambic">Asp-N_ambic</option>
-      <option value="Lys-C">Lys-C</option>
-      <option value="Trypsin" selected="true">Trypsin</option>
-      <option value="Trypsin/P">Trypsin/P</option>
-      <option value="Asp-N">Asp-N</option>
-      <option value="Lys-N">Lys-N</option>
+      <option value="CNBr">CNBr</option>
       <option value="Formic_acid">Formic_acid</option>
+      <option value="Lys-C">Lys-C</option>
+      <option value="Lys-N">Lys-N</option>
       <option value="Lys-C/P">Lys-C/P</option>
-      <option value="Asp-N/B">Asp-N/B</option>
       <option value="PepsinA">PepsinA</option>
+      <option value="TrypChymo">TrypChymo</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="V8-E">V8-E</option>
+      <option value="Arg-C">Arg-C</option>
       <option value="Arg-C/P">Arg-C/P</option>
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="iodosobenzoate">iodosobenzoate</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <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) "/>
+    <section name="FASTA" title="Options for FASTA output files" help="" expanded="false">
+      <param name="ID" argument="-FASTA:ID" display="radio" type="select" optional="false" label="Identifier to use for each peptide: copy from parent protein (parent); a consecutive number (number); parent ID + consecutive number (both)" help="">
+        <option value="parent" selected="true">parent</option>
+        <option value="number">number</option>
+        <option value="both">both</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="description" argument="-FASTA:description" display="radio" type="select" optional="false" label="Keep or remove the (possibly lengthy) FASTA header description" help="Keeping it can increase resulting FASTA file significantly">
+        <option value="remove" selected="true">remove</option>
+        <option value="keep">keep</option>
+        <expand macro="list_string_san"/>
+      </param>
+    </section>
+    <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="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="fasta"/>
+    <data name="out" label="${tool.name} on ${on_string}: out">
+      <change_format>
+        <when input="out_type" value="fasta" format="fasta"/>
+        <when input="out_type" value="idXML" format="idxml"/>
+      </change_format>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Digests a protein database in-silico.
+  <tests>
+    <expand macro="autotest_Digestor"/>
+    <expand macro="manutest_Digestor"/>
+  </tests>
+  <help><![CDATA[Digests a protein database in-silico.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_Digestor.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_Digestor.html]]></help>
+  <expand macro="references"/>
 </tool>