keep optional list params optional

with

galaxyproteomics#555
galaxyproteomics@fecd2cc
galaxyproteomics@ffdd5c5

optional (non file) parameters were rendered as required in the galaxy
xml

this commit tries to revert this, since it breaks the tests for Comet
Adapter, where the modification select parameters also allow to select
no parameter (and in the tests this is really done)

tools/openms/AccurateMassSearch.xml

@@ -139,13 +139,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
       </conditional>
     </section>
     <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
-      <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="false" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
-      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="false" label="Unit of mass error (ppm or Da)" help="">
+      <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
+      <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
         <option value="ppm" selected="true">ppm</option>
         <option value="Da">Da</option>
         <expand macro="list_string_san" name="mass_error_unit"/>
       </param>
-      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="false" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
+      <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
         <option value="positive" selected="true">positive</option>
         <option value="negative">negative</option>
         <option value="auto">auto</option>
@@ -154,7 +154,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
       <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
       <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
       <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/>
-      <param name="id_format" argument="-algorithm:id_format" type="select" optional="false" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
+      <param name="id_format" argument="-algorithm:id_format" type="select" optional="true" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
         <option value="legacy" selected="true">legacy</option>
         <option value="ID">ID</option>
         <expand macro="list_string_san" name="id_format"/>
@@ -165,7 +165,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
     </section>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" 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>

tools/openms/BaselineFilter.xml

@@ -42,13 +42,13 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
-    <param argument="-struc_elem_length" type="float" optional="false" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
-    <param argument="-struc_elem_unit" type="select" optional="false" label="Unit of 'struc_elem_length' paramete" help="">
+    <param argument="-struc_elem_length" type="float" optional="true" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
+    <param argument="-struc_elem_unit" type="select" optional="true" label="Unit of 'struc_elem_length' paramete" help="">
       <option value="Thomson" selected="true">Thomson</option>
       <option value="DataPoints">DataPoints</option>
       <expand macro="list_string_san" name="struc_elem_unit"/>
     </param>
-    <param argument="-method" type="select" optional="false" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
+    <param argument="-method" type="select" optional="true" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
       <option value="identity">identity</option>
       <option value="erosion">erosion</option>
       <option value="dilation">dilation</option>
@@ -63,7 +63,7 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" 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>

tools/openms/CVInspector.xml

@@ -80,13 +80,13 @@ ${' '.join(["'cv_files_cond.cv_files/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.el
       <expand macro="list_string_san" name="cv_names"/>
     </param>
     <param argument="-mapping_file" type="data" format="xml" optional="false" label="Mapping file in CVMapping (XML) format" help=" select xml data sets(s)"/>
-    <param argument="-ignore_cv" type="text" optional="false" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-ignore_cv" type="text" optional="true" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="ignore_cv"/>
       <expand macro="list_string_san" name="ignore_cv"/>
     </param>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" 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>

tools/openms/ClusterMassTraces.xml

@@ -42,15 +42,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
   </configfiles>
   <inputs>
     <param argument="-in" type="data" format="consensusxml" optional="false" label="Mass traces" help=" select consensusxml data sets(s)"/>
-    <param argument="-min_pearson_correlation" type="float" optional="false" value="0.7" label="Minimal pearson correlation score" help=""/>
-    <param argument="-min_peak_nr" type="integer" optional="false" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
-    <param argument="-max_lag" type="integer" optional="false" value="1" label="Maximal lag" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="false" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
-    <param argument="-max_intensity_cutoff" type="float" optional="false" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
-    <param argument="-add_precursor" type="float" optional="false" value="0.0" label="Add a precursor mass" help=""/>
+    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score" help=""/>
+    <param argument="-min_peak_nr" type="integer" optional="true" value="1" label="Minimal peak nr to output pseudo spectra" help=""/>
+    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time" help=""/>
+    <param argument="-max_intensity_cutoff" type="float" optional="true" value="0.0" label="Maximal intensity to be added to a spectrum" help=""/>
+    <param argument="-add_precursor" type="float" optional="true" value="0.0" label="Add a precursor mass" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" 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>

tools/openms/ClusterMassTracesByPrecursor.xml

@@ -48,15 +48,15 @@ python3 '$__tool_directory__/fill_ctd.py' '@[email protected]' '$args_json' '$hard
     <param argument="-in_ms1" type="data" format="consensusxml" optional="false" label="MS1 mass traces" help=" select consensusxml data sets(s)"/>
     <param argument="-in_swath" type="data" format="consensusxml" optional="false" label="MS2 / SWATH mass traces" help=" select consensusxml data sets(s)"/>
     <param argument="-assign_unassigned_to_all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign unassigned MS2 fragments to all precursors (only for ms1_centrif)" help=""/>
-    <param argument="-min_pearson_correlation" type="float" optional="false" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
-    <param argument="-max_lag" type="integer" optional="false" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
-    <param argument="-min_nr_ions" type="integer" optional="false" value="3" label="Minimal number of ions to report a spectrum" help=""/>
-    <param argument="-max_rt_apex_difference" type="float" optional="false" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
-    <param argument="-swath_lower" type="float" optional="false" value="0.0" label="Swath lower isolation window" help=""/>
-    <param argument="-swath_upper" type="float" optional="false" value="0.0" label="Swath upper isolation window" help=""/>
+    <param argument="-min_pearson_correlation" type="float" optional="true" value="0.7" label="Minimal pearson correlation score to match elution profiles to each othe" help=""/>
+    <param argument="-max_lag" type="integer" optional="true" value="1" label="Maximal lag" help="(e.g. by how many spectra the peak may be shifted at most). This parameter will depend on your chromatographic setup but a number between 1 and 3 is usually sensible"/>
+    <param argument="-min_nr_ions" type="integer" optional="true" value="3" label="Minimal number of ions to report a spectrum" help=""/>
+    <param argument="-max_rt_apex_difference" type="float" optional="true" value="5.0" label="Maximal difference of the apex in retention time (in seconds)" help="This is a hard parameter, all profiles further away will not be considered at all"/>
+    <param argument="-swath_lower" type="float" optional="true" value="0.0" label="Swath lower isolation window" help=""/>
+    <param argument="-swath_upper" type="float" optional="true" value="0.0" label="Swath upper isolation window" help=""/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="false" value="False" label="Enables the test mode (needed for internal use only)" 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>