annotate metanovo.xml @ 3:4a851c02f558 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380"
author galaxyp
date Tue, 29 Mar 2022 20:53:42 +0000
parents 08b5b0977c61
children 7a5ff5359b13
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08b5b0977c61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit e76dd65ed4a260c7e8b809478fcc6f3df02e8b5d"
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1 <tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
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2 <description>
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3 Produce targeted databases for mass spectrometry analysis.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
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7 </requirements>
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8 <macros>
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9 <token name="@TOOL_VERSION@">1.9.4</token>
3
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10 <token name="@VERSION_SUFFIX@">3</token>
0
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11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
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12 <import>macros_modifications.xml</import>
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13 </macros>
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14 <command>
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15 <![CDATA[
1
6066b729f9aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 1ae5ba121b7274f47ce5fc35db0965d3c9b0c451"
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16 #import re
0
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17 #set $mgf_dir = 'mgf_files'
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18 #set $fasta_dir = 'fasta_file'
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19 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier))
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20 mkdir $mgf_dir &&
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21 mkdir $fasta_dir &&
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22 ln -s '$input_fasta' '$fasta_dir/$fasta_name' &&
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23
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24 #if $input_type.type == "collection"
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25 #for $input_mgf_item in $input_type.input_mgf_collection:
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26 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_mgf_item.element_identifier))
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27 ln -s '$input_mgf_item' '$mgf_dir/$mgf_name' &&
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28 #end for
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29 #else
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30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier))
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31 ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' &&
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32 #end if
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33
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34 cat $metanovo_config > config.sh &&
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35 metanovo.sh config.sh
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36 ]]>
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37 </command>
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38
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39 <configfiles>
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40 <configfile name="metanovo_config"><![CDATA[#slurp
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41 #import re
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42 MGF_FOLDER=mgf_files
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43 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier))
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44 FASTA_FILE=fasta_file/'$fasta_name'
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45 OUTPUT_FOLDER=.
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46 CHUNKSIZE=$processing_control.CHUNKSIZE
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47 THREAD_LIMIT=$processing_control.THREAD_LIMIT
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48 JVM_Xmx='$processing_control.JVM_Xmx'
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49 JVM_Xms='$processing_control.JVM_Xms'
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50 mn_specificity='$metanovo_parameters.mn_specificity'
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51 mn_enzymes='$metanovo_parameters.mn_enzymes'
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52 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages
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53 dg_pepnovo=0
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54 dg_pnovo=0
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55 dg_novor=0
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56 dg_directag=1
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57 prec_tol=$spectrum_matching_parameters.prec_tol
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58 prec_ppm=$spectrum_matching_parameters.prec_ppm
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59 frag_tol=$spectrum_matching_parameters.frag_tol
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60 frag_ppm=$spectrum_matching_parameters.frag_ppm
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61 digestion=$spectrum_matching_parameters.digestion
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62 enzyme='$spectrum_matching_parameters.enzyme'
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63 specificity=$spectrum_matching_parameters.specificity
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64 mc='$spectrum_matching_parameters.mc'
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65 fixed_mods="$spectrum_matching_parameters.fixed_mods"
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66 variable_mods="$spectrum_matching_parameters.variable_mods"
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67 min_charge=$spectrum_matching_parameters.min_charge
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68 max_charge=$spectrum_matching_parameters.max_charge
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69 fi='$spectrum_matching_parameters.fi'
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70 ri='$spectrum_matching_parameters.ri'
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71 min_isotope='$spectrum_matching_parameters.min_isotope'
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72 max_isotope='$spectrum_matching_parameters.max_isotope'
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73 annotation_level=$spectrum_annotation.annotation_level
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74 annotation_high_resolution=$spectrum_annotation.annotation_high_resolution
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75 sequence_index_type=$sequence_matching.sequence_index_type
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76 sequence_matching_type=$sequence_matching.sequence_matching_type
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77 sequence_matching_x=$sequence_matching.sequence_matching_x
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78 import_peptide_length_min=$import_filters.import_peptide_length_min
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79 import_peptide_length_max=$import_filters.import_peptide_length_max
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80 import_precursor_mz_ppm=$import_filters.import_precursor_mz_ppm
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81 exclude_unknown_ptms=$import_filters.exclude_unknown_ptms
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82 ptm_score=$ptm_localization.ptm_score
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diff changeset
83 score_neutral_losses=$ptm_localization.score_neutral_losses
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
84 ptm_sequence_matching_type=$ptm_localization.ptm_sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
85 ptm_alignment=$ptm_localization.ptm_alignment
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
86 useGeneMapping=$gene_annotation.useGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
87 updateGeneMapping=$gene_annotation.updateGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
88 simplify_groups=$protein_inference.simplify_groups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
89 simplify_score=$protein_inference.simplify_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
90 simplify_enzymaticity=$protein_inference.simplify_enzymaticity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
91 simplify_evidence=$protein_inference.simplify_evidence
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
92 simplify_uncharacterized=$protein_inference.simplify_uncharacterized
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
93 psm_fdr=$validation_levels.psm_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
94 peptide_fdr=$validation_levels.peptide_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
95 protein_fdr=$validation_levels.protein_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
96 group_psms=$validation_levels.group_psms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
97 group_peptides=$validation_levels.group_peptides
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
98 merge_subgroups=$validation_levels.merge_subgroups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
99 protein_fraction_mw_confidence='$fraction_analysis.protein_fraction_mw_confidence'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
100 pepnovo_hitlist_length=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
101 pepnovo_estimate_charge=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
102 pepnovo_correct_prec_mass=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
103 pepnovo_discard_spectra=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
104 pepnovo_fragmentation_model='CID_IT_TRYP'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
105 pepnovo_generate_blast=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
106 directag_tic_cutoff=$directag.directag_tic_cutoff
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
107 directag_max_peak_count=$directag.directag_max_peak_count
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
108 directag_intensity_classes=$directag.directag_intensity_classes
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
109 directag_adjust_precursor=$directag.directag_adjust_precursor
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
110 directag_min_adjustment='$directag.directag_min_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
111 directag_max_adjustment='$directag.directag_max_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
112 directag_adjustment_step='$directag.directag_adjustment_step'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
113 directag_charge_states='$directag.directag_charge_states'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
114 directag_ms_charge_state='$directag.directag_ms_charge_state'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
115 directag_duplicate_spectra='$directag.directag_duplicate_spectra'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
116 directag_deisotoping='$directag.directag_deisotoping'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
117 directag_isotope_tolerance='$directag.directag_isotope_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
118 directag_complement_tolerance='$directag.directag_complement_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
119 directag_tag_length='$directag.directag_tag_length'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
120 directag_max_var_mods='$directag.directag_max_var_mods'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
121 directag_max_tag_count='$directag.directag_max_tag_count'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
122 directag_intensity_weight='$directag.directag_intensity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
123 directag_fidelity_weight='$directag.directag_fidelity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
124 directag_complement_weight='$directag.directag_complement_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
125 novor_fragmentation=HCD
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
126 novor_mass_analyzer=Trap
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
127 ]]></configfile>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
128 </configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
129
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
130 <inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
131 <conditional name="input_type">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
132 <param name="type" type="select" label="MGF Input Type" help="Submit either a single file, or a collection of files.">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
133 <option selected="true" value="single">Single file</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
134 <option value="collection">Collection</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
135 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
136 <when value="single">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
137 <param name="input_mgf" type="data" format="mgf" optional="true" label="MGF File" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
138 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
139 <when value="collection">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
140 <param name="input_mgf_collection" type="data_collection" optional="true" label="MGF Collection" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
141 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
142 </conditional>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
143
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
144 <param name="input_fasta" type="data" format="fasta" label="FASTA File" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
145
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
146 <section name="processing_control" expanded="False" title="Processing Control">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
147 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
148 <param name="THREAD_LIMIT" label="How many threads to use per node" value="2" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
149 <param name="JVM_Xmx" label="Maximum memory allocated to each Java thread" value="10000M" type="text" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
150 <param name="JVM_Xms" label="Minimum memory allocated to each Java thread" value="1024M" type="text" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
151 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
152 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
153 <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
154 <option selected="true" value="specific">specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
155 <option value="semi-specific">semi-specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
156 <option value="unspecific">unspecific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
157 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
158 <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
159 <option value="Trypsin">Trypsin</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
160 <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
161 <option value="Whole protein">Whole protein</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
162 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
163 <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
164 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
165 <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
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166 <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
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167 <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
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168 <option value="0">Da</option>
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169 <option selected="true" value="1">ppm</option>
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170 </param>
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171 <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
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172 <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
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173 <option selected="true" value="0">Da</option>
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174 <option value="1">ppm</option>
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175 </param>
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176 <param name="digestion" argument="-digestion" label="Digestion" type="select">
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177 <option selected="true" value="0">Enzyme</option>
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178 <option value="1">Unspecific</option>
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179 <option value="2">Whole Protein</option>
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180 </param>
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181 <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true">
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182 <option value="Trypsin">Trypsin</option>
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183 <option selected="true" value="Trypsin (no P rule)">Trypsin (no P rule)</option>
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184 <option value="Arg-C">Arg-C</option>
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185 <option value="Arg-C (no P rule)">Arg-C (no P rule)</option>
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186 <option value="Arg-N">Arg-N</option>
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187 <option value="Glu-C">Glu-C</option>
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188 <option value="Lys-C">Lys-C</option>
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189 <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
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190 <option value="Lys-N">Lys-N</option>
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191 <option value="Asp-N">Asp-N</option>
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192 <option value="Asp-N (ambic)">Asp-N (ambic)</option>
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193 <option value="Chymotrypsin">Chymotrypsin</option>
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194 <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
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195 <option value="Pepsin A">Pepsin A</option>
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196 <option value="CNBr">CNBr</option>
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197 <option value="Thermolysin">Thermolysin</option>
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198 <option value="LysargiNase">LysargiNase</option>
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199 </param>
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200 <param name="specificity" argument="-specificity" label="Specificity" type="select">
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201 <option selected="true" value="0">Specific</option>
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202 <option value="1">Semi-Specific</option>
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203 <option value="2">N-term Specific</option>
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204 <option value="3">C-term Specific</option>
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205 </param>
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206 <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;."/>
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207 <param name="fixed_mods" argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
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208 <expand macro="fixed_modifications"/>
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209 </param>
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210 <param name="variable_mods" argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
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211 <expand macro="variable_modifications"/>
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212 </param>
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213 <param name="min_charge" argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
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214 <param name="max_charge" argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
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215 <param name="fi" argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
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216 <param name="ri" argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
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217 <param name="min_isotope" argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
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218 <param name="max_isotope" argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
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219 </section>
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220 <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
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221 <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."/>
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222 <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"/>
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223 </section>
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224 <section name="sequence_matching" expanded="False" title="Sequence Matching">
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225 <param name="sequence_index_type" argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
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226 <param name="sequence_matching_type" argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
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227 <option value="0">Character Sequence</option>
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228 <option value="1">Amino Acids</option>
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229 <option selected="true" value="2">Indistinguishable Amino Acids</option>
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230 </param>
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231 <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"/>
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232 </section>
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233 <section name="import_filters" expanded="False" title="Import Filters">
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234 <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"/>
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235 <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"/>
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236 <param name="import_precursor_mz_ppm" argument="-import_precurosor_mz_ppm [sic]" label="Maximal precursor ion deviation unit" type="select">
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237 <option selected="true" value="0">Da</option>
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238 <option value="1">ppm</option>
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239 </param>
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240 <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"/>
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241 </section>
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242 <section name="ptm_localization" expanded="False" title="PTM Localization">
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243 <param name="ptm_score" argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
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244 <option value="0">A-score</option>
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245 <option selected="true" value="1">PhosphoRS</option>
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246 <option value="2">None</option>
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247 </param>
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248 <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"/>
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249 <param name="ptm_sequence_matching_type" argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
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250 <option value="0">Character Sequence</option>
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251 <option selected="true" value="1">Amino Acids</option>
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252 <option value="2">Indistinguishable Amino Acids</option>
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253 </param>
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254 <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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255 </section>
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256 <section name="gene_annotation" expanded="False" title="Gene Annotation">
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257 <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"/>
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258 <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
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259 </section>
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260 <section name="protein_inference" expanded="False" title="Protein Inference">
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261 <param name="simplify_groups" argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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262 <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"/>
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263 <param name="simplify_enzymaticity" argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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264 <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"/>
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265 <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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266 </section>
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267 <section name="validation_levels" expanded="False" title="Validation Levels">
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268 <param name="psm_fdr" argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
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269 <param name="peptide_fdr" argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
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270 <param name="protein_fdr" argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
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271 <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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272 <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"/>
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273 <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"/>
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274 </section>
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275 <section name="fraction_analysis" expanded="False" title="Fraction Analysis">
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276 <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"/>
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277 </section>
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278 <section name="directag" expanded="False" title="DirecTag">
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279 <param name="directag_tic_cutoff" argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
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280 <param name="directag_max_peak_count" argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
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281 <param name="directag_intensity_classes" argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
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282 <param name="directag_adjust_precursor" argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
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283 <param name="directag_min_adjustment" argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
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284 <param name="directag_max_adjustment" argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
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285 <param name="directag_adjustment_step" argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
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286 <param name="directag_charge_states" argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
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287 <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"/>
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288 <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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289 <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select">
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290 <option selected="true" value="0">No deisotoping</option>
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291 <option value="1">Precursor only</option>
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292 <option value="2">Precursor and candidate</option>
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293 </param>
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294 <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
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295 <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
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296 <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
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297 <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
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298 <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
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299 <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
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300 <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
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301 <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
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302 </section>
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303 </inputs>
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304 <outputs>
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305 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="MetaNovo Output FASTA"/>
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306 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="MetaNovo Output CSV"/>
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307 </outputs>
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308 <help><![CDATA[
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309 **MetaNovo**
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310
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311 MetaNovo searches MS/MS data against a FASTA database of known proteins.
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312
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313 Two outputs are produced:
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314
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315 - MetaNovo Output FASTA: the matching proteins produced by the search.
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316 - MetaNovo Output CSV: information about the job and other useful metadata.
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317
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318 Two inputs are required: an MGF file or files and a FASTA database file.
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319
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320 Two different input types are available for the MGF input. The correct input configuration depends on the desired use case, as outlined below:
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321
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322 ======================================================= =============
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323 Use case Configuration
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324 ======================================================= =============
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325 Single input MGF file, single output FASTA file **Single file** input with **Single dataset** selected
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326 Multiple input MGF files, multiple output FASTA files\* **Single file** input with **Multiple datasets** OR **Dataset collection** selected
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327 Multiple input MGF files, single output FASTA file **Collection** input
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328 ======================================================= =============
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329
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330 **\*** One for each MGF file.
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331
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332 In the second use case, a separate MetaNovo job is spawned for each input MGF. In the third use case, a single MetaNovo job runs with all MGF files in the collection as input.
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333
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334 If the third use case fails due to memory limitations, users are recommended to use the second option. The multiple output FASTA databases may be merged to generate a reduced, compact database.
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335 ]]>
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336 </help>
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337 <citations>
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338 <citation type="doi">10.1101/605550</citation>
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339 </citations>
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340 </tool>