--- a/ProteinQuantifier.xml	Fri May 17 10:08:09 2019 -0400
+++ b/ProteinQuantifier.xml	Thu Aug 27 19:36:58 2020 -0400
@@ -1,125 +1,162 @@
 <?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: [Quantitation]-->
-<tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.3.0">
+<tool id="ProteinQuantifier" name="ProteinQuantifier" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Compute peptide and protein abundances</description>
   <macros>
     <token name="@EXECUTABLE@">ProteinQuantifier</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[ProteinQuantifier
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+#if $protein_groups:
+  mkdir protein_groups &&
+  ln -s '$protein_groups' 'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)' &&
 #end if
-#if $param_protein_groups:
-  -protein_groups $param_protein_groups
-#end if
-#if $param_out:
-  -out $param_out
+#if $design:
+  mkdir design &&
+  ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
 #end if
-#if $param_peptide_out:
-  -peptide_out $param_peptide_out
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out &&
 #end if
-#if str($param_top):
-  -top $param_top
+#if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir peptide_out &&
+#end if
+#if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir mztab &&
 #end if
-#if $param_average:
-  -average
-  #if " " in str($param_average):
-    "$param_average"
-  #else
-    $param_average
-  #end if
-#end if
-#if $param_include_all:
-  -include_all
-#end if
-#if $param_filter_charge:
-  -filter_charge
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__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)'
+#if $protein_groups:
+  -protein_groups
+  'protein_groups/${re.sub("[^\w\-_]", "_", $protein_groups.element_identifier)}.$gxy2omsext($protein_groups.ext)'
 #end if
-#if $param_ratios:
-  -ratios
+#if $design:
+  -design
+  'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
 #end if
-#if $param_ratiosSILAC:
-  -ratiosSILAC
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out
+  'out/output.${gxy2omsext("csv")}'
 #end if
-#if $param_consensus_normalize:
-  -consensus:normalize
+#if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -peptide_out
+  'peptide_out/output.${gxy2omsext("csv")}'
 #end if
-#if $param_consensus_fix_peptides:
-  -consensus:fix_peptides
+#if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -mztab
+  'mztab/output.${gxy2omsext("mztab")}'
 #end if
-#if $param_format_separator:
-  -format:separator     "$param_format_separator"
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
 #end if
-#if $param_format_quoting:
-  -format:quoting
-  #if " " in str($param_format_quoting):
-    "$param_format_quoting"
-  #else
-    $param_format_quoting
-  #end if
+
+## Postprocessing
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out/output.${gxy2omsext("csv")}' '$out'
 #end if
-#if $param_format_replacement:
-  -format:replacement     "$param_format_replacement"
+#if "peptide_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'peptide_out/output.${gxy2omsext("csv")}' '$peptide_out'
+#end if
+#if "mztab_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'mztab/output.${gxy2omsext("mztab")}' '$mztab'
 #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="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/>
-    <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification"/>
-    <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top) "/>
-    <param name="param_average" display="radio" type="select" optional="False" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average) ">
+    <param name="in" argument="-in" type="data" format="consensusxml,featurexml,idxml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml data sets(s)"/>
+    <param name="protein_groups" argument="-protein_groups" type="data" format="idxml" optional="true" label="Protein inference results for the identification runs that were used to annotate the input" help="(e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter).. Information about indistinguishable proteins will be used for protein quantification select idxml data sets(s)"/>
+    <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/>
+    <param name="top" argument="-top" type="integer" optional="true" min="0" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help=""/>
+    <param name="average" argument="-average" display="radio" type="select" optional="false" label="Averaging method used to compute protein abundances from peptide abundances" help="">
       <option value="median" selected="true">median</option>
       <option value="mean">mean</option>
       <option value="weighted_mean">weighted_mean</option>
       <option value="sum">sum</option>
-    </param>
-    <param name="param_include_all" display="radio" type="boolean" truevalue="-include_all" falsevalue="" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all) "/>
-    <param name="param_filter_charge" display="radio" type="boolean" truevalue="-filter_charge" falsevalue="" checked="false" optional="True" label="Distinguish between charge states of a peptide" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states"/>
-    <param name="param_ratios" display="radio" type="boolean" truevalue="-ratios" falsevalue="" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output" help="(-ratios) Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
-    <param name="param_ratiosSILAC" display="radio" type="boolean" truevalue="-ratiosSILAC" falsevalue="" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
-    <param name="param_consensus_normalize" display="radio" type="boolean" truevalue="-consensus:normalize" falsevalue="" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize) "/>
-    <param name="param_consensus_fix_peptides" display="radio" type="boolean" truevalue="-consensus:fix_peptides" falsevalue="" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
-    <param name="param_format_separator" type="text" size="30" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_format_quoting" display="radio" type="select" optional="False" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
-      <option value="none">none</option>
-      <option value="double" selected="true">double</option>
-      <option value="escape">escape</option>
+    <param name="include_all" argument="-include_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help=""/>
+    <param name="best_charge_and_fraction" argument="-best_charge_and_fraction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Distinguish between fraction and charge states of a peptide" help="For peptides, abundances will be reported separately for each fraction and charge;. for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions).. By default, abundances are summed over all charge states"/>
+    <param name="greedy_group_resolution" argument="-greedy_group_resolution" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Pre-process identifications with greedy resolution of shared peptides based on the protein group probabilities" help="(Only works with an idXML file given as protein_groups parameter)"/>
+    <param name="ratios" argument="-ratios" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios of the abundance values to the output" help="Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
+    <param name="ratiosSILAC" argument="-ratiosSILAC" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add the log2 ratios for a triple SILAC experiment to the output" help="Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
+    <section name="consensus" title="Additional options for consensus maps (and identification results comprising multiple runs)" help="" expanded="false">
+      <param name="normalize" argument="-consensus:normalize" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Scale peptide abundances so that medians of all samples are equal" help=""/>
+      <param name="fix_peptides" argument="-consensus:fix_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the same peptides for protein quantification across all samples" help="With 'top 0', all peptides that occur in every sample are considered.. Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,. breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
+    </section>
+    <section name="format" title="Output formatting options" help="" expanded="false">
+      <param name="separator" argument="-format:separator" type="text" optional="true" value="" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="">
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="quoting" argument="-format:quoting" display="radio" type="select" optional="false" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+        <option value="none">none</option>
+        <option value="double" selected="true">double</option>
+        <option value="escape">escape</option>
+        <expand macro="list_string_san"/>
+      </param>
+      <param name="replacement" argument="-format:replacement" type="text" optional="true" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="">
+        <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="false">
+      <option value="out_FLAG">out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
+      <option value="peptide_out_FLAG">peptide_out (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
+      <option value="mztab_FLAG">mztab (If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing)</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <param name="param_format_replacement" type="text" size="30" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </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>
   </inputs>
   <outputs>
-    <data name="param_out" format="tabular"/>
-    <data name="param_peptide_out" format="tabular"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="csv">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="peptide_out" label="${tool.name} on ${on_string}: peptide_out" format="csv">
+      <filter>OPTIONAL_OUTPUTS is not None and "peptide_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="mztab" label="${tool.name} on ${on_string}: mztab" format="mztab">
+      <filter>OPTIONAL_OUTPUTS is not None and "mztab_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="stdout" format="txt" label="${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>Compute peptide and protein abundances
+  <tests>
+    <expand macro="autotest_ProteinQuantifier"/>
+    <expand macro="manutest_ProteinQuantifier"/>
+  </tests>
+  <help><![CDATA[Compute peptide and protein abundances
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinQuantifier.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_ProteinQuantifier.html]]></help>
+  <expand macro="references"/>
 </tool>