--- a/PeptideIndexer.xml	Fri Nov 06 20:41:30 2020 +0000
+++ b/PeptideIndexer.xml	Thu Dec 01 19:11:03 2022 +0000
@@ -1,13 +1,11 @@
 <?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="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="PeptideIndexer" name="PeptideIndexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Refreshes the protein references for all peptide hits.</description>
   <macros>
     <token name="@EXECUTABLE@">PeptideIndexer</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -49,57 +47,58 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
-    <param name="fasta" argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
-    <param name="decoy_string" argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
-      <expand macro="list_string_san"/>
+    <param argument="-in" type="data" format="idxml" optional="false" label="Input idXML file containing the identifications" help=" select idxml data sets(s)"/>
+    <param argument="-fasta" type="data" format="fasta" optional="true" label="Input sequence database in FASTA format" help="Leave empty for using the same DB as used for the input idXML (this might fail). Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir' select fasta data sets(s)"/>
+    <param argument="-decoy_string" type="text" optional="true" value="" label="String that was appended (or prefixed - see 'decoy_string_position' flag below) to the accessions in the protein database to indicate decoy proteins" help="If empty (default), it's determined automatically (checking for common terms, both as prefix and suffix)">
+      <expand macro="list_string_san" name="decoy_string"/>
     </param>
-    <param name="decoy_string_position" argument="-decoy_string_position" display="radio" type="select" optional="false" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
+    <param argument="-decoy_string_position" type="select" optional="true" label="Is the 'decoy_string' prepended (prefix) or appended (suffix) to the protein accession" help="(ignored if decoy_string is empty)">
       <option value="prefix" selected="true">prefix</option>
       <option value="suffix">suffix</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="decoy_string_position"/>
     </param>
-    <param name="missing_decoy_action" argument="-missing_decoy_action" display="radio" type="select" optional="false" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
+    <param argument="-missing_decoy_action" type="select" optional="true" label="Action to take if NO peptide was assigned to a decoy protein (which indicates wrong database or decoy string): 'error' (exit with error, no output), 'warn' (exit with success, warning message), 'silent' (no action is taken, not even a warning)" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="silent">silent</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="missing_decoy_action"/>
     </param>
-    <param name="write_protein_sequence" argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
-    <param name="write_protein_description" argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
-    <param name="keep_unreferenced_proteins" argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
-    <param name="unmatched_action" argument="-unmatched_action" display="radio" type="select" optional="false" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
+    <param argument="-write_protein_sequence" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein sequences are stored as well" help=""/>
+    <param argument="-write_protein_description" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, the protein description is stored as well" help=""/>
+    <param argument="-keep_unreferenced_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If set, protein hits which are not referenced by any peptide are kept" help=""/>
+    <param argument="-unmatched_action" type="select" optional="true" label="If peptide sequences cannot be matched to any protein: 1) raise an error; 2) warn (unmatched PepHits will miss target/decoy annotation with downstream problems); 3) remove the hit" help="">
       <option value="error" selected="true">error</option>
       <option value="warn">warn</option>
       <option value="remove">remove</option>
-      <expand macro="list_string_san"/>
+      <expand macro="list_string_san" name="unmatched_action"/>
     </param>
-    <param name="aaa_max" argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are B, J, Z and X!"/>
-    <param name="mismatches_max" argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
-    <param name="IL_equivalent" argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
+    <param argument="-aaa_max" type="integer" optional="true" min="0" max="10" value="3" label="Maximal number of ambiguous amino acids (AAAs) allowed when matching to a protein database with AAAs" help="AAAs are 'B', 'J', 'Z' and 'X'"/>
+    <param argument="-mismatches_max" type="integer" optional="true" min="0" max="10" value="0" label="Maximal number of mismatched (mm) amino acids allowed when matching to a protein database" help="The required runtime is exponential in the number of mm's; apply with care. MM's are allowed in addition to AAA's"/>
+    <param argument="-IL_equivalent" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="Also occurrences of 'J' will be treated as 'I' thus avoiding ambiguous matching"/>
     <section name="enzyme" title="" help="" expanded="false">
-      <param name="name" argument="-enzyme:name" type="select" optional="false" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
+      <param name="name" argument="-enzyme:name" type="select" optional="true" label="Enzyme which determines valid cleavage sites -" help="e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P). Default: deduce from input">
         <option value="auto" selected="true">auto</option>
+        <option value="Arg-C">Arg-C</option>
+        <option value="Arg-C/P">Arg-C/P</option>
+        <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="Chymotrypsin">Chymotrypsin</option>
         <option value="Chymotrypsin/P">Chymotrypsin/P</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="Trypsin/P">Trypsin/P</option>
+        <option value="V8-DE">V8-DE</option>
+        <option value="V8-E">V8-E</option>
+        <option value="leukocyte elastase">leukocyte elastase</option>
         <option value="proline endopeptidase">proline endopeptidase</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="staphylococcal protease/D">staphylococcal protease/D</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="leukocyte elastase">leukocyte elastase</option>
-        <option value="Arg-C">Arg-C</option>
-        <option value="Arg-C/P">Arg-C/P</option>
-        <option value="Asp-N">Asp-N</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>
@@ -108,25 +107,24 @@
         <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="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="PepsinA">PepsinA</option>
+        <option value="TrypChymo">TrypChymo</option>
         <option value="Trypsin">Trypsin</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="name"/>
       </param>
-      <param name="specificity" argument="-enzyme:specificity" display="radio" type="select" optional="false" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
+      <param name="specificity" argument="-enzyme:specificity" type="select" optional="true" label="Specificity of the enzyme" help="Default: deduce from input..   'full': both internal cleavage sites must match..   'semi': one of two internal cleavage sites must match..   'none': allow all peptide hits no matter their context (enzyme is irrelevant)">
         <option value="auto" selected="true">auto</option>
         <option value="full">full</option>
         <option value="semi">semi</option>
         <option value="none">none</option>
-        <expand macro="list_string_san"/>
+        <expand macro="list_string_san" name="specificity"/>
       </param>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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 argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
+      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -139,13 +137,400 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_PeptideIndexer"/>
-    <expand macro="manutest_PeptideIndexer"/>
+  <tests><!-- TOPP_PeptideIndexer_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_1_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_2_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="true"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_3_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="true"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_4 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_4_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="true"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="0"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_5 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_5_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_6 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_2.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_6_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="3"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_7 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_3.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_7_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value="DECOY_"/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="full"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_8 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_3.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_8_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="semi"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_9 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_3.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_9_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="remove"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_10 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_10_input.idXML"/>
+      <param name="fasta" value="PeptideIndexer_10_input.fasta"/>
+      <output name="out" file="PeptideIndexer_10_output.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="true"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="error"/>
+      <param name="aaa_max" value="3"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="true"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_12 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_1.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_12_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="warn"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_13 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="empty.idXML"/>
+      <param name="fasta" value="PeptideIndexer_1.fasta"/>
+      <output name="out" file="PeptideIndexer_13_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="false"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="error"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="auto"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_PeptideIndexer_14 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PeptideIndexer_14.idXML"/>
+      <param name="fasta" value="PeptideIndexer_2.fasta"/>
+      <output name="out" file="PeptideIndexer_14_out.tmp.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <param name="decoy_string" value=""/>
+      <param name="decoy_string_position" value="prefix"/>
+      <param name="missing_decoy_action" value="error"/>
+      <param name="write_protein_sequence" value="true"/>
+      <param name="write_protein_description" value="false"/>
+      <param name="keep_unreferenced_proteins" value="false"/>
+      <param name="unmatched_action" value="error"/>
+      <param name="aaa_max" value="4"/>
+      <param name="mismatches_max" value="0"/>
+      <param name="IL_equivalent" value="false"/>
+      <section name="enzyme">
+        <param name="name" value="auto"/>
+        <param name="specificity" value="none"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Refreshes the protein references for all peptide hits.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PeptideIndexer.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PeptideIndexer.html]]></help>
   <expand macro="references"/>
 </tool>