--- a/PhosphoScoring.xml	Fri May 17 09:18:13 2019 -0400
+++ b/PhosphoScoring.xml	Wed Sep 09 19:45:14 2020 +0000
@@ -1,68 +1,84 @@
 <?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: [ID Processing]-->
-<tool id="PhosphoScoring" name="PhosphoScoring" version="2.3.0">
+<tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
   <macros>
     <token name="@EXECUTABLE@">PhosphoScoring</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[PhosphoScoring
+  <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($in.ext)' &&
+mkdir id &&
+ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+mkdir out &&
+
+## Main program call
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_id:
-  -id $param_id
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_fragment_mass_tolerance:
-  -fragment_mass_tolerance $param_fragment_mass_tolerance
-#end if
-#if $param_fragment_mass_unit:
-  -fragment_mass_unit
-  #if " " in str($param_fragment_mass_unit):
-    "$param_fragment_mass_unit"
-  #else
-    $param_fragment_mass_unit
-  #end if
-#end if
-#if $param_max_peptide_length:
-  -max_peptide_length $param_max_peptide_length
-#end if
-#if $param_max_num_perm:
-  -max_num_perm $param_max_num_perm
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-id
+'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
+-out
+'out/output.${gxy2omsext("idxml")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("idxml")}' '$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="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/>
-    <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/>
-    <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/>
-    <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) ">
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
+    <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/>
+    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
+    <param name="fragment_mass_unit" argument="-fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/>
-    <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/>
-    <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="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/>
+      <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/>
+      <param name="unambiguous_score" argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/>
+      <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="idxml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Scores potential phosphorylation sites in order to localize the most probable sites.
+  <tests>
+    <expand macro="autotest_PhosphoScoring"/>
+    <expand macro="manutest_PhosphoScoring"/>
+  </tests>
+  <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PhosphoScoring.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_PhosphoScoring.html]]></help>
+  <expand macro="references"/>
 </tool>