--- a/DatabaseSuitability.xml	Fri Nov 06 20:31:13 2020 +0000
+++ b/DatabaseSuitability.xml	Thu Dec 01 19:02:20 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: []-->
-<tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<!--Proposed Tool Section: [Quality Control]-->
+<tool id="DatabaseSuitability" name="DatabaseSuitability" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">DatabaseSuitability</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -22,6 +20,10 @@
 ln -s '$in_spec' 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)' &&
 mkdir in_novo &&
 ln -s '$in_novo' 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)' &&
+mkdir database &&
+ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
+mkdir novo_database &&
+ln -s '$novo_database' 'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -38,6 +40,10 @@
 'in_spec/${re.sub("[^\w\-_]", "_", $in_spec.element_identifier)}.$gxy2omsext($in_spec.ext)'
 -in_novo
 'in_novo/${re.sub("[^\w\-_]", "_", $in_novo.element_identifier)}.$gxy2omsext($in_novo.ext)'
+-database
+'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
+-novo_database
+'novo_database/${re.sub("[^\w\-_]", "_", $novo_database.element_identifier)}.$gxy2omsext($novo_database.ext)'
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out
   'out/output.${gxy2omsext("tabular")}'
@@ -58,18 +64,25 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in_id" argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from peptide search with combined database with added de novo peptide" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/>
-    <param name="in_spec" argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/>
-    <param name="in_novo" argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/>
+    <param argument="-in_id" type="data" format="idxml" optional="false" label="Input idXML file from a peptide identification search with a combined database" help="PeptideIndexer is needed, FDR is forbidden select idxml data sets(s)"/>
+    <param argument="-in_spec" type="data" format="mzml" optional="false" label="Input MzML file used for the peptide identification" help=" select mzml data sets(s)"/>
+    <param argument="-in_novo" type="data" format="idxml" optional="false" label="Input idXML file containing de novo peptides (unfiltered)" help=" select idxml data sets(s)"/>
+    <param argument="-database" type="data" format="fasta" optional="false" label="Input FASTA file of the database in question" help=" select fasta data sets(s)"/>
+    <param argument="-novo_database" type="data" format="fasta" optional="false" label="Input deNovo sequences derived from MzML given in 'in_spec' concatenated to one FASTA entry" help=" select fasta data sets(s)"/>
     <section name="algorithm" title="Parameter section for the suitability calculation algorithm" help="" expanded="false">
       <param name="no_rerank" argument="-algorithm:no_rerank" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if you want to disable re-ranking" help="Cases, where a de novo peptide scores just higher than the database peptide, are overlooked and counted as a de novo hit. This might underestimate the database quality"/>
       <param name="reranking_cutoff_percentile" argument="-algorithm:reranking_cutoff_percentile" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Swap a top-scoring deNovo hit with a lower scoring DB hit if their xcorr score difference is in the given percentile of all score differences between the first two decoy hits of a PSM" help="The lower the value the lower the decoy cut-off will be. Therefore it will be harder for a lower scoring DB hit to be re-ranked to the top"/>
       <param name="FDR" argument="-algorithm:FDR" type="float" optional="true" min="0.0" max="1.0" value="0.01" label="Filter peptide hits based on this q-value" help="(e.g., 0.05 = 5 % FDR)"/>
+      <param name="number_of_subsampled_runs" argument="-algorithm:number_of_subsampled_runs" type="integer" optional="true" min="0" value="1" label="Controls how many runs should be done for calculating corrected suitability" help="(0 : number of runs will be estimated automaticly) ATTENTION: For each run a seperate ID-search is performed. This can result in some serious run time"/>
+      <param name="keep_search_files" argument="-algorithm:keep_search_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you wish to keep the files used by and produced by the internal ID search" help=""/>
+      <param name="disable_correction" argument="-algorithm:disable_correction" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to disable the calculation of the corrected suitability" help=""/>
+      <param name="force" argument="-algorithm:force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to enforce re-ranking when no cross correlation score is present" help="For re-ranking the default score found at each peptide hit is used. Use with care!"/>
     </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="-novo_threshold" type="float" optional="true" min="0.0" value="60.0" label="Minimum score a de novo sequence has to have to be defined as 'correct'" help="The default of 60 is proven to be a good estimate for sequences generated by Novor"/>
+      <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">
@@ -88,12 +101,97 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_DatabaseSuitability"/>
-    <expand macro="manutest_DatabaseSuitability"/>
+  <tests><!-- TOPP_DatabaseSuitability_1 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="novo_threshold" value="60.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <param name="database" value="DatabaseSuitability_database.fasta"/>
+      <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
+      <output name="out" file="DatabaseSuitability_out_1.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.01"/>
+        <param name="number_of_subsampled_runs" value="1"/>
+        <param name="keep_search_files" value="false"/>
+        <param name="disable_correction" value="false"/>
+        <param name="force" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_DatabaseSuitability_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="novo_threshold" value="60.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <param name="database" value="DatabaseSuitability_database.fasta"/>
+      <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
+      <output name="out" file="DatabaseSuitability_out_2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.01"/>
+        <param name="FDR" value="0.05"/>
+        <param name="number_of_subsampled_runs" value="1"/>
+        <param name="keep_search_files" value="false"/>
+        <param name="disable_correction" value="false"/>
+        <param name="force" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+    <!-- TOPP_DatabaseSuitability_3 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="novo_threshold" value="60.0"/>
+        <param name="force" value="false"/>
+        <param name="test" value="true"/>
+      </section>
+      <param name="in_id" value="DatabaseSuitability_in_id.idXML"/>
+      <param name="in_spec" value="DatabaseSuitability_in_spec.mzML"/>
+      <param name="in_novo" value="DatabaseSuitability_in_novo.idXML"/>
+      <param name="database" value="DatabaseSuitability_database.fasta"/>
+      <param name="novo_database" value="DatabaseSuitability_novo_database.FASTA"/>
+      <output name="out" file="DatabaseSuitability_out_3.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <section name="algorithm">
+        <param name="no_rerank" value="false"/>
+        <param name="reranking_cutoff_percentile" value="0.5"/>
+        <param name="FDR" value="0.5"/>
+        <param name="number_of_subsampled_runs" value="1"/>
+        <param name="keep_search_files" value="false"/>
+        <param name="disable_correction" value="false"/>
+        <param name="force" value="false"/>
+      </section>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help><![CDATA[Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra.
 
-]]></help>
+
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DatabaseSuitability.html]]></help>
   <expand macro="references"/>
 </tool>