--- a/metanovo.xml	Fri Apr 22 13:31:08 2022 +0000
+++ b/metanovo.xml	Sat May 11 16:46:46 2024 +0000
@@ -2,15 +2,18 @@
   <description>
     Produce targeted databases for mass spectrometry analysis.
   </description>
-  <requirements>
-    <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
-  </requirements>
   <macros>
     <token name="@TOOL_VERSION@">1.9.4</token>
     <token name="@VERSION_SUFFIX@">4</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
     <import>macros_modifications.xml</import>
   </macros>
+  <xrefs>
+    <xref type="bio.tools">metanovo</xref>
+  </xrefs>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
+  </requirements>
   <command>
     <![CDATA[
       #import re
@@ -152,35 +155,35 @@
       <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
     </section>
     <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
-      <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">
+      <param argument="-mn_specificity" label="Enzyme Specificity" type="select">
         <option selected="true" value="specific">specific</option>
         <option value="semi-specific">semi-specific</option>
         <option value="unspecific">unspecific</option>
       </param>
-      <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select">
+      <param argument="-mn_enzymes" label="Enzyme Rule" type="select">
         <option value="Trypsin">Trypsin</option>
         <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>
         <option value="Whole protein">Whole protein</option>
       </param>
-      <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
+      <param argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
     </section>
     <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
-      <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
-      <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
+      <param argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
+      <param argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
         <option value="0">Da</option>
         <option selected="true" value="1">ppm</option>
       </param>
-      <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
-      <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
+      <param argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
+      <param argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
         <option selected="true" value="0">Da</option>
         <option value="1">ppm</option>
       </param>
-      <param name="digestion" argument="-digestion" label="Digestion" type="select">
+      <param argument="-digestion" label="Digestion" type="select">
         <option selected="true" value="0">Enzyme</option>
         <option value="1">Unspecific</option>
         <option value="2">Whole Protein</option>
       </param>
-      <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true">
+      <param argument="-enzyme" label="Enzyme" type="select" multiple="true">
         <option value="Trypsin">Trypsin</option>
         <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option>
         <option value="Arg-C">Arg-C</option>
@@ -199,108 +202,108 @@
         <option value="Thermolysin">Thermolysin</option>
         <option value="LysargiNase">LysargiNase</option>
       </param>
-      <param name="specificity" argument="-specificity" label="Specificity" type="select">
+      <param argument="-specificity" label="Specificity" type="select">
           <option selected="true" value="0">Specific</option>
           <option value="1">Semi-Specific</option>
           <option value="2">N-term Specific</option>
           <option value="3">C-term Specific</option>
       </param>
-      <param name="mc" argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/>
-      <param name="fixed_mods" argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
+      <param argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. &quot;2, 1&quot;."/>
+      <param argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
         <expand macro="fixed_modifications"/>
       </param>
-      <param name="variable_mods" argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
+      <param argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
         <expand macro="variable_modifications"/>
       </param>
-      <param name="min_charge" argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
-      <param name="max_charge" argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
-      <param name="fi" argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
-      <param name="ri" argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
-      <param name="min_isotope" argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
-      <param name="max_isotope" argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
+      <param argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
+      <param argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
+      <param argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
+      <param argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
+      <param argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
+      <param argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
     </section>
     <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
-      <param name="annotation_level" argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
-      <param name="annotation_high_resolution" argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
+      <param argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="sequence_matching" expanded="False" title="Sequence Matching">
-      <param name="sequence_index_type" argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
-      <param name="sequence_matching_type" argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
+      <param argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
+      <param argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
           <option value="0">Character Sequence</option>
           <option value="1">Amino Acids</option>
           <option selected="true" value="2">Indistinguishable Amino Acids</option>
       </param>
-      <param name="sequence_matching_x" argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
+      <param argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
     </section>
     <section name="import_filters" expanded="False" title="Import Filters">
-      <param name="import_peptide_length_min" argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
-      <param name="import_peptide_length_max" argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
-      <param name="import_precursor_mz_ppm" argument="-import_precurosor_mz_ppm [sic]" label="Maximal precursor ion deviation unit" type="select">
+      <param argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
+      <param argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
+      <param argument="-import_precursor_mz_ppm" label="Maximal precursor ion deviation unit" type="select">
         <option selected="true" value="0">Da</option>
         <option value="1">ppm</option>
       </param>
-      <param name="exclude_unknown_ptms" argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="ptm_localization" expanded="False" title="PTM Localization">
-      <param name="ptm_score" argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
+      <param argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
         <option value="0">A-score</option>
         <option selected="true" value="1">PhosphoRS</option>
         <option value="2">None</option>
       </param>
-      <param name="score_neutral_losses" argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="ptm_sequence_matching_type" argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
+      <param argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
           <option value="0">Character Sequence</option>
           <option selected="true" value="1">Amino Acids</option>
           <option value="2">Indistinguishable Amino Acids</option>
       </param>
-      <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="gene_annotation" expanded="False" title="Gene Annotation">
-      <param name="useGeneMapping" argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true"  help="UniProt databases only"/>
-      <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
+      <param argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true"  help="UniProt databases only"/>
+      <param argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
     </section>
     <section name="protein_inference" expanded="False" title="Protein Inference">
-      <param name="simplify_groups" argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_score" argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_enzymaticity" argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_evidence" argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="validation_levels" expanded="False" title="Validation Levels">
-      <param name="psm_fdr" argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
-      <param name="peptide_fdr" argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
-      <param name="protein_fdr" argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
-      <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="group_peptides" argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="merge_subgroups" argument="-group_peptides" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
+      <param argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-merge_subgroups" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
     </section>
     <section name="fraction_analysis" expanded="False" title="Fraction Analysis">
-      <param name="protein_fraction_mw_confidence" argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
+      <param argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
     </section>
     <section name="directag" expanded="False" title="DirecTag">
-      <param name="directag_tic_cutoff" argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
-      <param name="directag_max_peak_count" argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
-      <param name="directag_intensity_classes" argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
-      <param name="directag_adjust_precursor" argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="directag_min_adjustment" argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
-      <param name="directag_max_adjustment" argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
-      <param name="directag_adjustment_step" argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
-      <param name="directag_charge_states" argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
-      <param name="directag_ms_charge_state" argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
-      <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
-      <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select">
+      <param argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
+      <param argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
+      <param argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
+      <param argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
+      <param argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
+      <param argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
+      <param argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
+      <param argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
+      <param argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
+      <param argument="-directag_deisotoping" label="Deisotoping mode" type="select">
         <option selected="true" value="0">No deisotoping</option>
         <option value="1">Precursor only</option>
         <option value="2">Precursor and candidate</option>
       </param>
-      <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
-      <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
-      <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
-      <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
-      <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
-      <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
-      <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
-      <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
+      <param argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
+      <param argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
+      <param argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
+      <param argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
+      <param argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
+      <param argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
     </section>
   </inputs>
   <outputs>