Mercurial > repos > galaxyp > metanovo

annotate metanovo.xml @ 0:9025f297a511 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
author galaxyp
date Tue, 29 Mar 2022 16:54:19 +0000
parents
children 6066b729f9aa
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
1 <tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy0" profile="20.09">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
2 <description>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
3 Produce targeted databases for mass spectrometry analysis.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
4 </description>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
5 <requirements>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
7 </requirements>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
8 <macros>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
9 <token name="@TOOL_VERSION@">1.9.4</token>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
10 <token name="@VERSION_SUFFIX@">0</token>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
11 <token name="@SUBSTITUTION_RX@">[^\w\-\.]</token>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
12 <import>macros_modifications.xml</import>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
13 </macros>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
14 <command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
15 <![CDATA[
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
16 #set $mgf_dir = 'mgf_files'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
17 #set $fasta_dir = 'fasta_file'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
18 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier))
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
19 mkdir $mgf_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
20 mkdir $fasta_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
21 ln -s '$input_fasta' '$fasta_dir/$fasta_name' &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
22
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
23 #if $input_type.type == "collection"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
24 #set mgf_names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $input_type.input_mgf_collection]
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
25 #for $mgf_name in $mgf_names:
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
26 ln -s '$input' '$mgf_dir/$mgf_name' &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
27 #end for
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
28 #else
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
29 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier))
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
30 ln -s '$input_mgf' '$mgf_dir/$mgf_name' &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
31 #end if
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
32
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
33 cat $metanovo_config > config.sh &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
34 metanovo.sh config.sh
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
35 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
36 </command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
37
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
38 <configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
39 <configfile name="metanovo_config"><![CDATA[#slurp
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
40 #import re
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
41 MGF_FOLDER=mgf_files
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
42 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_fasta.element_identifier))
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
43 FASTA_FILE=fasta_file/'$fasta_name'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
44 OUTPUT_FOLDER=.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
45 CHUNKSIZE=$processing_control.CHUNKSIZE
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
46 THREAD_LIMIT=$processing_control.THREAD_LIMIT
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
47 JVM_Xmx='$processing_control.JVM_Xmx'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
48 JVM_Xms='$processing_control.JVM_Xms'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
49 mn_specificity='$metanovo_parameters.mn_specificity'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
50 mn_enzymes='$metanovo_parameters.mn_enzymes'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
51 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
52 dg_pepnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
53 dg_pnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
54 dg_novor=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
55 dg_directag=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
56 prec_tol=$spectrum_matching_parameters.prec_tol
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
57 prec_ppm=$spectrum_matching_parameters.prec_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
58 frag_tol=$spectrum_matching_parameters.frag_tol
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
59 frag_ppm=$spectrum_matching_parameters.frag_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
60 digestion=$spectrum_matching_parameters.digestion
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
61 enzyme='$spectrum_matching_parameters.enzyme'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
62 specificity=$spectrum_matching_parameters.specificity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
63 mc='$spectrum_matching_parameters.mc'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
64 fixed_mods="$spectrum_matching_parameters.fixed_mods"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
65 variable_mods="$spectrum_matching_parameters.variable_mods"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
66 min_charge=$spectrum_matching_parameters.min_charge
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
67 max_charge=$spectrum_matching_parameters.max_charge
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
68 fi='$spectrum_matching_parameters.fi'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
69 ri='$spectrum_matching_parameters.ri'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
70 min_isotope='$spectrum_matching_parameters.min_isotope'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
71 max_isotope='$spectrum_matching_parameters.max_isotope'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
72 annotation_level=$spectrum_annotation.annotation_level
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
73 annotation_high_resolution=$spectrum_annotation.annotation_high_resolution
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
74 sequence_index_type=$sequence_matching.sequence_index_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
75 sequence_matching_type=$sequence_matching.sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
76 sequence_matching_x=$sequence_matching.sequence_matching_x
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
77 import_peptide_length_min=$import_filters.import_peptide_length_min
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
78 import_peptide_length_max=$import_filters.import_peptide_length_max
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
79 import_precursor_mz_ppm=$import_filters.import_precursor_mz_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
80 exclude_unknown_ptms=$import_filters.exclude_unknown_ptms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
81 ptm_score=$ptm_localization.ptm_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
82 score_neutral_losses=$ptm_localization.score_neutral_losses
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
83 ptm_sequence_matching_type=$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
84 ptm_alignment=$ptm_localization.ptm_alignment
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
85 useGeneMapping=$gene_annotation.useGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
86 updateGeneMapping=$gene_annotation.updateGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
87 simplify_groups=$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
88 simplify_score=$protein_inference.simplify_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
89 simplify_enzymaticity=$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
90 simplify_evidence=$protein_inference.simplify_evidence
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
91 simplify_uncharacterized=$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
92 psm_fdr=$validation_levels.psm_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
93 peptide_fdr=$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
94 protein_fdr=$validation_levels.protein_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
95 group_psms=$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
96 group_peptides=$validation_levels.group_peptides
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
97 merge_subgroups=$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
98 protein_fraction_mw_confidence='$fraction_analysis.protein_fraction_mw_confidence'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
99 pepnovo_hitlist_length=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
100 pepnovo_estimate_charge=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
101 pepnovo_correct_prec_mass=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
102 pepnovo_discard_spectra=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
103 pepnovo_fragmentation_model='CID_IT_TRYP'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
104 pepnovo_generate_blast=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
105 directag_tic_cutoff=$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
106 directag_max_peak_count=$directag.directag_max_peak_count
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
107 directag_intensity_classes=$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
108 directag_adjust_precursor=$directag.directag_adjust_precursor
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
109 directag_min_adjustment='$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
110 directag_max_adjustment='$directag.directag_max_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
111 directag_adjustment_step='$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
112 directag_charge_states='$directag.directag_charge_states'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
113 directag_ms_charge_state='$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
114 directag_duplicate_spectra='$directag.directag_duplicate_spectra'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
115 directag_deisotoping='$directag.directag_deisotoping'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
116 directag_isotope_tolerance='$directag.directag_isotope_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
117 directag_complement_tolerance='$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
118 directag_tag_length='$directag.directag_tag_length'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
119 directag_max_var_mods='$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
120 directag_max_tag_count='$directag.directag_max_tag_count'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
121 directag_intensity_weight='$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
122 directag_fidelity_weight='$directag.directag_fidelity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
123 directag_complement_weight='$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
124 novor_fragmentation=HCD
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
125 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
126 ]]></configfile>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
127 </configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
128
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
129 <inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
130 <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
131 <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
132 <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
133 <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
134 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
135 <when value="single">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
136 <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
137 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
138 <when value="collection">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
139 <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
140 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
141 </conditional>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
142
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
143 <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
144
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
145 <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
146 <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
147 <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
148 <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
149 <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
150 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
151 <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
152 <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
153 <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
154 <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
155 <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
156 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
157 <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
158 <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
159 <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
160 <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
161 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
162 <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
163 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
164 <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
parents:
diff changeset
165 <param name="prec_tol" argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
166 <param name="prec_ppm" argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
167 <option value="0">Da</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
168 <option selected="true" value="1">ppm</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
169 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
170 <param name="frag_tol" argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
171 <param name="frag_ppm" argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
172 <option selected="true" value="0">Da</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
173 <option value="1">ppm</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
174 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
175 <param name="digestion" argument="-digestion" label="Digestion" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
176 <option selected="true" value="0">Enzyme</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
177 <option value="1">Unspecific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
178 <option value="2">Whole Protein</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
179 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
180 <param name="enzyme" argument="-enzyme" label="Enzyme" type="select" multiple="true">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
181 <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
182 <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
183 <option value="Arg-C">Arg-C</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
184 <option value="Arg-C (no P rule)">Arg-C (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
185 <option value="Arg-N">Arg-N</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
186 <option value="Glu-C">Glu-C</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
187 <option value="Lys-C">Lys-C</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
188 <option value="Lys-C (no P rule)">Lys-C (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
189 <option value="Lys-N">Lys-N</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
190 <option value="Asp-N">Asp-N</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
191 <option value="Asp-N (ambic)">Asp-N (ambic)</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
192 <option value="Chymotrypsin">Chymotrypsin</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
193 <option value="Chymotrypsin (no P rule)">Chymotrypsin (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
194 <option value="Pepsin A">Pepsin A</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
195 <option value="CNBr">CNBr</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
196 <option value="Thermolysin">Thermolysin</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
197 <option value="LysargiNase">LysargiNase</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
198 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
199 <param name="specificity" argument="-specificity" label="Specificity" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
200 <option selected="true" value="0">Specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
201 <option value="1">Semi-Specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
202 <option value="2">N-term Specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
203 <option value="3">C-term Specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
204 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
205 <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;."/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
206 <param name="fixed_mods" argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
207 <expand macro="fixed_modifications"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
208 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
209 <param name="variable_mods" argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
210 <expand macro="variable_modifications"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
211 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
212 <param name="min_charge" argument="-min_charge" label="Minimal charge to search for" 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
213 <param name="max_charge" argument="-max_charge" label="Maximal charge to search for" value="4" 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
214 <param name="fi" argument="-fi" label="Type of forward ion searched" value="b" 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
215 <param name="ri" argument="-ri" label="Type of rewind ion searched" value="y" 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
216 <param name="min_isotope" argument="-min_isotope" label="Minimum precursor isotope" value="0" 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
217 <param name="max_isotope" argument="-max_isotope" label="Maximum precursor isotope" value="1" 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
218 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
219 <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
220 <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."/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
221 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
222 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
223 <section name="sequence_matching" expanded="False" title="Sequence Matching">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
224 <param name="sequence_index_type" argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" 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
225 <param name="sequence_matching_type" argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
226 <option value="0">Character Sequence</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
227 <option value="1">Amino Acids</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
228 <option selected="true" value="2">Indistinguishable Amino Acids</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
229 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
230 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
231 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
232 <section name="import_filters" expanded="False" title="Import Filters">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
233 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
234 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
235 <param name="import_precursor_mz_ppm" argument="-import_precurosor_mz_ppm [sic]" label="Maximal precursor ion deviation unit" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
236 <option selected="true" value="0">Da</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
237 <option value="1">ppm</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
238 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
239 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
240 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
241 <section name="ptm_localization" expanded="False" title="PTM Localization">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
242 <param name="ptm_score" argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
243 <option value="0">A-score</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
244 <option selected="true" value="1">PhosphoRS</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
245 <option value="2">None</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
246 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
247 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
248 <param name="ptm_sequence_matching_type" argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
249 <option value="0">Character Sequence</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
250 <option selected="true" value="1">Amino Acids</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
251 <option value="2">Indistinguishable Amino Acids</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
252 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
253 <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
254 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
255 <section name="gene_annotation" expanded="False" title="Gene Annotation">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
256 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
257 <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
258 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
259 <section name="protein_inference" expanded="False" title="Protein Inference">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
260 <param name="simplify_groups" argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
261 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
262 <param name="simplify_enzymaticity" argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
263 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
264 <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
265 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
266 <section name="validation_levels" expanded="False" title="Validation Levels">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
267 <param name="psm_fdr" argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" 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
268 <param name="peptide_fdr" argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" 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
269 <param name="protein_fdr" argument="-protein_fdr" label="FDR at the protein level in percent" value="1" 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
270 <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
271 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
272 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
273 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
274 <section name="fraction_analysis" expanded="False" title="Fraction Analysis">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
275 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
276 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
277 <section name="directag" expanded="False" title="DirecTag">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
278 <param name="directag_tic_cutoff" argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" 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
279 <param name="directag_max_peak_count" argument="-directag_max_peak_count" label="Max peak count" value="400" 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
280 <param name="directag_intensity_classes" argument="-directag_intensity_classes" label="Number of intensity classes" value="3" 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
281 <param name="directag_adjust_precursor" argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
282 <param name="directag_min_adjustment" argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
283 <param name="directag_max_adjustment" argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
284 <param name="directag_adjustment_step" argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
285 <param name="directag_charge_states" argument="-directag_charge_states" label="Number of charge states considered" value="3" 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
286 <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"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
287 <param name="directag_duplicate_spectra" argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
288 <param name="directag_deisotoping" argument="-directag_deisotoping" label="Deisotoping mode" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
289 <option selected="true" value="0">No deisotoping</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
290 <option value="1">Precursor only</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
291 <option value="2">Precursor and candidate</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
292 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
293 <param name="directag_isotope_tolerance" argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
294 <param name="directag_complement_tolerance" argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
295 <param name="directag_tag_length" argument="-directag_tag_length" label="Tag length" value="4" 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
296 <param name="directag_max_var_mods" argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" 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
297 <param name="directag_max_tag_count" argument="-directag_max_tag_count" label="Maximum tag count" value="5" 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
298 <param name="directag_intensity_weight" argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
299 <param name="directag_fidelity_weight" argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
300 <param name="directag_complement_weight" argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
301 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
302 </inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
303 <outputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
304 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="MetaNovo Output FASTA"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
305 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="MetaNovo Output CSV"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
306 </outputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
307 <help><![CDATA[
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
308 **MetaNovo**
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
309
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
310 MetaNovo searches MS/MS data against a FASTA database of known proteins.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
311
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
312 Two outputs are produced:
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
313
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
314 - MetaNovo Output FASTA: the matching proteins produced by the search.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
315 - MetaNovo Output CSV: information about the job and other useful metadata.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
316
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
317 Two inputs are required: an MGF file or files and a FASTA database file.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
318
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
319 Two different input types are available for the MGF input. The correct input configuration depends on the desired use case, as outlined below:
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
320
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
321 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
322 Use case Configuration
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
323 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
324 Single input MGF file, single output FASTA file **Single file** input with **Single dataset** selected
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
325 Multiple input MGF files, multiple output FASTA files\* **Single file** input with **Multiple datasets** OR **Dataset collection** selected
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
326 Multiple input MGF files, single output FASTA file **Collection** input
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
327 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
328
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
329 **\*** One for each MGF file.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
330
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
331 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.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
332
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
333 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.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
334 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
335 </help>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
336 <citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
337 <citation type="doi">10.1101/605550</citation>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
338 </citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89"
galaxyp
parents:
diff changeset
339 </tool>