metanovo: metanovo.xml annotate

annotate metanovo.xml @ 3:4a851c02f558 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380"

author	galaxyp
date	Tue, 29 Mar 2022 20:53:42 +0000
parents	08b5b0977c61
children	7a5ff5359b13

rev	line source
2 08b5b0977c61 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit e76dd65ed4a260c7e8b809478fcc6f3df02e8b5d" galaxyp parents: 1 diff changeset	1 <tool id="metanovo" name="MetaNovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
0 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>
3 4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	10 <token name="@VERSION_SUFFIX@">3</token>
0 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[
1 6066b729f9aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 1ae5ba121b7274f47ce5fc35db0965d3c9b0c451" galaxyp parents: 0 diff changeset	16 #import re
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	17 #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	18 #set $fasta_dir = 'fasta_file'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	19 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($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	20 mkdir $mgf_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	21 mkdir $fasta_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	22 ln -s '$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	23
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	24 #if $input_type.type == "collection"
3 4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	25 #for $input_mgf_item in $input_type.input_mgf_collection:
4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	26 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_mgf_item.element_identifier))
4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	27 ln -s '$input_mgf_item' '$mgf_dir/$mgf_name' &&
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	28 #end for
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	29 #else
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	30 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($input_type.input_mgf.element_identifier))
3 4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	31 ln -s '$input_type.input_mgf' '$mgf_dir/$mgf_name' &&
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	32 #end if
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	33
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	34 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	35 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	36 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	37 </command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	38
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	39 <configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	40 <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	41 #import re
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	42 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	43 #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	44 FASTA_FILE=fasta_file/'$fasta_name'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	45 OUTPUT_FOLDER=.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	46 CHUNKSIZE=$processing_control.CHUNKSIZE
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	47 THREAD_LIMIT=$processing_control.THREAD_LIMIT
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	48 JVM_Xmx='$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	49 JVM_Xms='$processing_control.JVM_Xms'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	50 mn_specificity='$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	51 mn_enzymes='$metanovo_parameters.mn_enzymes'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	52 mn_max_missed_cleavages=$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	53 dg_pepnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	54 dg_pnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	55 dg_novor=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	56 dg_directag=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	57 prec_tol=$spectrum_matching_parameters.prec_tol
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	58 prec_ppm=$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	59 frag_tol=$spectrum_matching_parameters.frag_tol
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	60 frag_ppm=$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	61 digestion=$spectrum_matching_parameters.digestion
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	62 enzyme='$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	63 specificity=$spectrum_matching_parameters.specificity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	64 mc='$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	65 fixed_mods="$spectrum_matching_parameters.fixed_mods"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	66 variable_mods="$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	67 min_charge=$spectrum_matching_parameters.min_charge
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	68 max_charge=$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	69 fi='$spectrum_matching_parameters.fi'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	70 ri='$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	71 min_isotope='$spectrum_matching_parameters.min_isotope'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	72 max_isotope='$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	73 annotation_level=$spectrum_annotation.annotation_level
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	74 annotation_high_resolution=$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	75 sequence_index_type=$sequence_matching.sequence_index_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	76 sequence_matching_type=$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	77 sequence_matching_x=$sequence_matching.sequence_matching_x
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	78 import_peptide_length_min=$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	79 import_peptide_length_max=$import_filters.import_peptide_length_max
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	80 import_precursor_mz_ppm=$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	81 exclude_unknown_ptms=$import_filters.exclude_unknown_ptms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	82 ptm_score=$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	83 score_neutral_losses=$ptm_localization.score_neutral_losses
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	84 ptm_sequence_matching_type=$ptm_localization.ptm_sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	85 ptm_alignment=$ptm_localization.ptm_alignment
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	86 useGeneMapping=$gene_annotation.useGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	87 updateGeneMapping=$gene_annotation.updateGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	88 simplify_groups=$protein_inference.simplify_groups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	89 simplify_score=$protein_inference.simplify_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	90 simplify_enzymaticity=$protein_inference.simplify_enzymaticity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	91 simplify_evidence=$protein_inference.simplify_evidence
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	92 simplify_uncharacterized=$protein_inference.simplify_uncharacterized
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	93 psm_fdr=$validation_levels.psm_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	94 peptide_fdr=$validation_levels.peptide_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	95 protein_fdr=$validation_levels.protein_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	96 group_psms=$validation_levels.group_psms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	97 group_peptides=$validation_levels.group_peptides
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	98 merge_subgroups=$validation_levels.merge_subgroups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	99 protein_fraction_mw_confidence='$fraction_analysis.protein_fraction_mw_confidence'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	100 pepnovo_hitlist_length=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	101 pepnovo_estimate_charge=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	102 pepnovo_correct_prec_mass=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	103 pepnovo_discard_spectra=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	104 pepnovo_fragmentation_model='CID_IT_TRYP'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	105 pepnovo_generate_blast=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	106 directag_tic_cutoff=$directag.directag_tic_cutoff
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	107 directag_max_peak_count=$directag.directag_max_peak_count
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	108 directag_intensity_classes=$directag.directag_intensity_classes
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	109 directag_adjust_precursor=$directag.directag_adjust_precursor
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	110 directag_min_adjustment='$directag.directag_min_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	111 directag_max_adjustment='$directag.directag_max_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	112 directag_adjustment_step='$directag.directag_adjustment_step'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	113 directag_charge_states='$directag.directag_charge_states'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	114 directag_ms_charge_state='$directag.directag_ms_charge_state'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	115 directag_duplicate_spectra='$directag.directag_duplicate_spectra'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	116 directag_deisotoping='$directag.directag_deisotoping'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	117 directag_isotope_tolerance='$directag.directag_isotope_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	118 directag_complement_tolerance='$directag.directag_complement_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	119 directag_tag_length='$directag.directag_tag_length'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	120 directag_max_var_mods='$directag.directag_max_var_mods'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	121 directag_max_tag_count='$directag.directag_max_tag_count'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	122 directag_intensity_weight='$directag.directag_intensity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	123 directag_fidelity_weight='$directag.directag_fidelity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	124 directag_complement_weight='$directag.directag_complement_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	125 novor_fragmentation=HCD
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	126 novor_mass_analyzer=Trap
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	127 ]]></configfile>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	128 </configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	129
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	130 <inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	131 <conditional name="input_type">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	132 <param name="type" type="select" label="MGF Input Type" help="Submit either a single file, or a collection of files.">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	133 <option selected="true" value="single">Single file</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	134 <option value="collection">Collection</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	135 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	136 <when value="single">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	137 <param name="input_mgf" type="data" format="mgf" optional="true" label="MGF File" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	138 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	139 <when value="collection">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	140 <param name="input_mgf_collection" type="data_collection" optional="true" label="MGF Collection" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	141 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	142 </conditional>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	143
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	144 <param name="input_fasta" type="data" format="fasta" label="FASTA File" />
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	145
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	146 <section name="processing_control" expanded="False" title="Processing Control">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	147 <param name="CHUNKSIZE" label="Size to split fasta for parallel processing" value="100000" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	148 <param name="THREAD_LIMIT" label="How many threads to use per node" value="2" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	149 <param name="JVM_Xmx" label="Maximum memory allocated to each Java thread" value="10000M" type="text" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	150 <param name="JVM_Xms" label="Minimum memory allocated to each Java thread" value="1024M" type="text" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	151 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	152 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	153 <param name="mn_specificity" argument="-mn_specificity" label="Enzyme Specificity" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	154 <option selected="true" value="specific">specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	155 <option value="semi-specific">semi-specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	156 <option value="unspecific">unspecific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	157 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	158 <param name="mn_enzymes" argument="-mn_enzymes" label="Enzyme Rule" type="select">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	159 <option value="Trypsin">Trypsin</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	160 <option selected="true" value="Trypsin, no P rule">Trypsin, no P rule</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	161 <option value="Whole protein">Whole protein</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	162 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	163 <param name="mn_max_missed_cleavages" argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	164 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	165 <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	166 <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	167 <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	168 <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	169 <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	170 </param>
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_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	172 <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	173 <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	174 <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	175 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	176 <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	177 <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	178 <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	179 <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	180 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	200 <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	201 <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	202 <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	203 <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	204 <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	205 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	206 <param name="mc" argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. "2, 1"."/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	207 <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	208 <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	209 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	210 <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	211 <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	212 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	213 <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	214 <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	215 <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	216 <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	217 <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	218 <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	219 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	220 <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	221 <param name="annotation_level" argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	222 <param name="annotation_high_resolution" argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	223 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	224 <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	225 <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	226 <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	227 <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	228 <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	229 <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	230 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	231 <param name="sequence_matching_x" argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	232 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	233 <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	234 <param name="import_peptide_length_min" argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
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_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	236 <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	237 <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	238 <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	239 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	240 <param name="exclude_unknown_ptms" argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	241 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	242 <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	243 <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	244 <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	245 <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	246 <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	247 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	248 <param name="score_neutral_losses" argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	249 <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	250 <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	251 <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	252 <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	253 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	254 <param name="ptm_alignment" argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	255 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	256 <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	257 <param name="useGeneMapping" argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	258 <param name="updateGeneMapping" argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	259 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	260 <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	261 <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	262 <param name="simplify_score" argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
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_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	264 <param name="simplify_evidence" argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	265 <param name="simplify_uncharacterized" argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	266 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	267 <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	268 <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	269 <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	270 <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	271 <param name="group_psms" argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	272 <param name="group_peptides" argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	273 <param name="merge_subgroups" argument="-group_peptides" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	274 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	275 <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	276 <param name="protein_fraction_mw_confidence" argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	277 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <param name="directag_ms_charge_state" argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
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_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	289 <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	290 <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	291 <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	292 <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	293 </param>
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_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	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	303 </inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	304 <outputs>
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_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	306 <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	307 </outputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	308 <help><![CDATA[
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	309 MetaNovo
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	310
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	311 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	312
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	313 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	314
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	315 - 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	316 - 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	317
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	318 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	319
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	320 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	321
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	322 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	323 Use case Configuration
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	324 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	325 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	326 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	327 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	328 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	329
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	330 \* 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	331
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	332 In the second use case, a separate MetaNovo job is spawned for each input MGF. In the third use case, a single MetaNovo job runs with all MGF files in the collection as input.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	333
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	334 If the third use case fails due to memory limitations, users are recommended to use the second option. The multiple output FASTA databases may be merged to generate a reduced, compact database.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	335 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	336 </help>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	337 <citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	338 <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	339 </citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	340 </tool>

Mercurial > repos > galaxyp > metanovo

annotate metanovo.xml @ 3:4a851c02f558 draft