--- a/PeakPickerIterative.xml	Fri May 17 10:03:11 2019 -0400
+++ b/PeakPickerIterative.xml	Thu Aug 27 19:46:58 2020 -0400
@@ -1,76 +1,81 @@
 <?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: [Signal processing and preprocessing]-->
-<tool id="PeakPickerIterative" name="PeakPickerIterative" version="2.3.0">
+<tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Finds mass spectrometric peaks in profile mass spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">PeakPickerIterative</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[PeakPickerIterative
+  <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($in.ext)'
+-out
+'out/output.${gxy2omsext("mzml")}'
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_algorithm_signal_to_noise_:
-  -algorithm:signal_to_noise_ $param_algorithm_signal_to_noise_
-#end if
-#if $param_algorithm_peak_width:
-  -algorithm:peak_width $param_algorithm_peak_width
-#end if
-#if $param_algorithm_ms1_only:
-  -algorithm:ms1_only
-#end if
-#if $param_algorithm_clear_meta_data:
-  -algorithm:clear_meta_data
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-    #if $adv_opts.param_algorithm_spacing_difference:
-  -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference
-#end if
-    #if $adv_opts.param_algorithm_sn_bin_count_:
-  -algorithm:sn_bin_count_ $adv_opts.param_algorithm_sn_bin_count_
-#end if
-    #if $adv_opts.param_algorithm_nr_iterations_:
-  -algorithm:nr_iterations_ $adv_opts.param_algorithm_nr_iterations_
-#end if
-    #if $adv_opts.param_algorithm_sn_win_len_:
-  -algorithm:sn_win_len_ $adv_opts.param_algorithm_sn_win_len_
-#end if
-    #if $adv_opts.param_algorithm_check_width_internally:
-  -algorithm:check_width_internally
-#end if
-#end if
-]]></command>
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("mzml")}' '$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" help="(-in) "/>
-    <param name="param_algorithm_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_) "/>
-    <param name="param_algorithm_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
-    <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/>
-    <param name="param_algorithm_clear_meta_data" display="radio" type="boolean" truevalue="-algorithm:clear_meta_data" falsevalue="" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data) "/>
-    <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) "/>
-      <param name="param_algorithm_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="(-spacing_difference) The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
-      <param name="param_algorithm_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help="(-sn_bin_count_) "/>
-      <param name="param_algorithm_nr_iterations_" type="integer" min="1" optional="True" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help="(-nr_iterations_) "/>
-      <param name="param_algorithm_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help="(-sn_win_len_) "/>
-      <param name="param_algorithm_check_width_internally" display="radio" type="boolean" truevalue="-algorithm:check_width_internally" falsevalue="" checked="false" optional="True" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help="(-check_width_internally) "/>
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
+      <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
+      <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
+      <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
+      <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" optional="true" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
+      <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" optional="true" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
+      <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" optional="true" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
+      <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/>
+      <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
+      <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/>
+    </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="mzml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Finds mass spectrometric peaks in profile mass spectra.
+  <tests>
+    <expand macro="autotest_PeakPickerIterative"/>
+    <expand macro="manutest_PeakPickerIterative"/>
+  </tests>
+  <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PeakPickerIterative.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_PeakPickerIterative.html]]></help>
+  <expand macro="references"/>
 </tool>