metanovo: metanovo.xml annotate

annotate metanovo.xml @ 4:7a5ff5359b13 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8"

author	galaxyp
date	Fri, 22 Apr 2022 13:31:08 +0000
parents	4a851c02f558
children	d6dcd3173bdf

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>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	10 <token name="@VERSION_SUFFIX@">4</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
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	34 ## the number of threads should be number of available threads-1 according to the docs
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	35 threads=\${GALAXY_SLOTS:-3} &&
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	36 if [ \$threads -gt 1 ]; then
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	37 (( threads-- ));
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	38 fi &&
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	39 echo "THREAD_LIMIT=\$threads" >> config.sh &&
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	40
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	41 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	42 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	43 </command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	44
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	45 <configfiles>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	46 <configfile filename="config.sh"><![CDATA[#slurp
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	47 #import re
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	48 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	49 #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	50 FASTA_FILE=fasta_file/'$fasta_name'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	51 OUTPUT_FOLDER=.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	52 CHUNKSIZE=$processing_control.CHUNKSIZE
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	53 JVM_Xmx='10000M'
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	54 JVM_Xms='1024M'
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	55 mn_specificity='$metanovo_parameters.mn_specificity'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	56 mn_enzymes='$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	57 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	58 dg_pepnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	59 dg_pnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	60 dg_novor=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	61 dg_directag=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	62 prec_tol=$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	63 prec_ppm=$spectrum_matching_parameters.prec_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	64 frag_tol=$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	65 frag_ppm=$spectrum_matching_parameters.frag_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	66 digestion=$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	67 enzyme='$spectrum_matching_parameters.enzyme'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	68 specificity=$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	69 mc='$spectrum_matching_parameters.mc'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	70 fixed_mods="$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	71 variable_mods="$spectrum_matching_parameters.variable_mods"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	72 min_charge=$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	73 max_charge=$spectrum_matching_parameters.max_charge
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	74 fi='$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	75 ri='$spectrum_matching_parameters.ri'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	76 min_isotope='$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	77 max_isotope='$spectrum_matching_parameters.max_isotope'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	78 annotation_level=$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	79 annotation_high_resolution=$spectrum_annotation.annotation_high_resolution
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	80 sequence_index_type=$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	81 sequence_matching_type=$sequence_matching.sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	82 sequence_matching_x=$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	83 import_peptide_length_min=$import_filters.import_peptide_length_min
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	84 import_peptide_length_max=$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	85 import_precursor_mz_ppm=$import_filters.import_precursor_mz_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	86 exclude_unknown_ptms=$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	87 ptm_score=$ptm_localization.ptm_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	88 score_neutral_losses=$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	89 ptm_sequence_matching_type=$ptm_localization.ptm_sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	90 ptm_alignment=$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	91 useGeneMapping=$gene_annotation.useGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	92 updateGeneMapping=$gene_annotation.updateGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	93 simplify_groups=$protein_inference.simplify_groups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	94 simplify_score=$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	95 simplify_enzymaticity=$protein_inference.simplify_enzymaticity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	96 simplify_evidence=$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	97 simplify_uncharacterized=$protein_inference.simplify_uncharacterized
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	98 psm_fdr=$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	99 peptide_fdr=$validation_levels.peptide_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	100 protein_fdr=$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	101 group_psms=$validation_levels.group_psms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	102 group_peptides=$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	103 merge_subgroups=$validation_levels.merge_subgroups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	104 protein_fraction_mw_confidence='$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	105 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	106 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	107 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	108 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	109 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	110 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	111 directag_tic_cutoff=$directag.directag_tic_cutoff
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	112 directag_max_peak_count=$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	113 directag_intensity_classes=$directag.directag_intensity_classes
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	114 directag_adjust_precursor=$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	115 directag_min_adjustment='$directag.directag_min_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	116 directag_max_adjustment='$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	117 directag_adjustment_step='$directag.directag_adjustment_step'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	118 directag_charge_states='$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	119 directag_ms_charge_state='$directag.directag_ms_charge_state'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	120 directag_duplicate_spectra='$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	121 directag_deisotoping='$directag.directag_deisotoping'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	122 directag_isotope_tolerance='$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	123 directag_complement_tolerance='$directag.directag_complement_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	124 directag_tag_length='$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	125 directag_max_var_mods='$directag.directag_max_var_mods'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	126 directag_max_tag_count='$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	127 directag_intensity_weight='$directag.directag_intensity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	128 directag_fidelity_weight='$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	129 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	130 novor_fragmentation=HCD
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	131 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	132 ]]></configfile>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	133 </configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	134
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	135 <inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	136 <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	137 <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	138 <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	139 <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	140 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	141 <when value="single">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	142 <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	143 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	144 <when value="collection">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	145 <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	146 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	147 </conditional>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	148
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	149 <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	150
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	151 <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	152 <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	153 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	154 <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	155 <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	156 <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	157 <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	158 <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	159 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	160 <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	161 <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	162 <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	163 <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	164 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	165 <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	166 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	167 <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	168 <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	169 <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	170 <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	171 <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	172 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	173 <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	174 <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	175 <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	176 <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	177 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	178 <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	179 <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	180 <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	181 <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	182 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	183 <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	184 <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	185 <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	186 <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	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	202 <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	203 <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	204 <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	205 <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	206 <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	207 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	208 <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	209 <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	210 <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	211 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	212 <param name="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	213 <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	214 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	215 <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	216 <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	217 <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	218 <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	219 <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	220 <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	221 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	222 <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	223 <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	224 <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	225 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	226 <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	227 <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	228 <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	229 <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	230 <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	231 <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	232 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	233 <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	234 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	235 <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	236 <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	237 <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	238 <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	239 <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	240 <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	241 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	242 <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	243 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	244 <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	245 <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	246 <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	247 <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	248 <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	249 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	250 <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	251 <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	252 <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	253 <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	254 <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	255 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	256 <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	257 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	258 <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	259 <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	260 <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	261 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	262 <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	263 <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	264 <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	265 <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	266 <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	267 <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	268 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	277 <section name="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	278 <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	279 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 </param>
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_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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	305 </inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	306 <outputs>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	307 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	308 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${tool.name} on ${on_string}: CSV"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	309 </outputs>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	310 <tests>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	311 <test expect_num_outputs="2">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	312 <param name="input_mgf" value="sample_data_1.mgf" ftype="mgf"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	313 <param name="input_fasta" value="sample_fasta_single.fasta" ftype="fasta"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	314 <output name="output_csv" ftype="csv">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	315 <assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	316 <!-- Check header. -->
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	317 <has_text text=",index,Accession,Record,ID,PeptideCount,Peptides,ScanCount,Scans,Organism,Length,File,Sample sample_data_1 (msms),SAF sample_data_1,NSAF sample_data_1,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	318 </assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	319 </output>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	320 <output name="output_fasta" ftype="fasta" file="sample_output_single.fasta"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	321 </test>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	322 <test expect_num_outputs="2">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	323 <param name="type" value="collection"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	324 <param name="input_mgf_collection">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	325 <collection type="list">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	326 <element name="sample_data_1.mgf" value="sample_data_1.mgf" />
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	327 <element name="sample_data_2.mgf" value="sample_data_2.mgf" />
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	328 </collection>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	329 </param>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	330 <param name="input_fasta" value="sample_fasta_collection.fasta" ftype="fasta"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	331 <output name="output_csv" ftype="csv">
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	332 <assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	333 <!-- Check header. -->
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	334 <has_text text=",index,Accession,File,ID,Length,Organism,PeptideCount,Peptides,Record,SAF sample_data_1,SAF sample_data_2,Sample sample_data_1 (msms),Sample sample_data_2 (msms),ScanCount,Scans,NSAF sample_data_1,NSAF sample_data_2,Summed_NSAF,Protein_Prob,Organism_Prob,MSMS_Percent,Combined_Prob"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	335 </assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	336 </output>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	337 <output name="output_fasta" ftype="fasta" file="sample_output_collection.fasta"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	338 </test>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	339 </tests>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	340 <help><![CDATA[
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	341 MetaNovo
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	342
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	343 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	344
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	345 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	346
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	347 - 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	348 - 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	349
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	350 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	351
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	352 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	353
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	354 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	355 Use case Configuration
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	356 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	357 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	358 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	359 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	360 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	361
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	362 \* 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	363
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	364 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	365
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	366 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	367 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	368 </help>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	369 <citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	370 <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	371 </citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	372 </tool>

Mercurial > repos > galaxyp > metanovo

annotate metanovo.xml @ 4:7a5ff5359b13 draft