metanovo: metanovo.xml annotate

annotate metanovo.xml @ 5:d6dcd3173bdf draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199

author	galaxyp
date	Sat, 11 May 2024 16:46:46 +0000
parents	7a5ff5359b13
children

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 <macros>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	6 <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	7 <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	8 <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	9 <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	10 </macros>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	11 <xrefs>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	12 <xref type="bio.tools">metanovo</xref>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	13 </xrefs>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	14 <requirements>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	15 <requirement type="package" version="@TOOL_VERSION@">metanovo</requirement>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	16 </requirements>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	17 <command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	18 <![CDATA[
1 6066b729f9aa "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 1ae5ba121b7274f47ce5fc35db0965d3c9b0c451" galaxyp parents: 0 diff changeset	19 #import re
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	20 #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	21 #set $fasta_dir = 'fasta_file'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	22 #set fasta_name = re.sub('@SUBSTITUTION_RX@', '_', str($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	23 mkdir $mgf_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	24 mkdir $fasta_dir &&
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	25 ln -s '$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	26
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	27 #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	28 #for $input_mgf_item in $input_type.input_mgf_collection:
4a851c02f558 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 420ef6b0ee91e44ed354366a55575c1aa504e380" galaxyp parents: 2 diff changeset	29 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($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	30 ln -s '$input_mgf_item' '$mgf_dir/$mgf_name' &&
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	31 #end for
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	32 #else
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	33 #set mgf_name = re.sub('@SUBSTITUTION_RX@', '_', str($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	34 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	35 #end if
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	36
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	37 ## 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	38 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	39 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	40 (( threads-- ));
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	41 fi &&
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	42 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	43
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	44 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	45 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	46 </command>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	47
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	48 <configfiles>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	49 <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	50 #import re
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	51 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	52 #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	53 FASTA_FILE=fasta_file/'$fasta_name'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	54 OUTPUT_FOLDER=.
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	55 CHUNKSIZE=$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	56 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	57 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	58 mn_specificity='$metanovo_parameters.mn_specificity'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	59 mn_enzymes='$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	60 mn_max_missed_cleavages=$metanovo_parameters.mn_max_missed_cleavages
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	61 dg_pepnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	62 dg_pnovo=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	63 dg_novor=0
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	64 dg_directag=1
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	65 prec_tol=$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	66 prec_ppm=$spectrum_matching_parameters.prec_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	67 frag_tol=$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	68 frag_ppm=$spectrum_matching_parameters.frag_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	69 digestion=$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	70 enzyme='$spectrum_matching_parameters.enzyme'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	71 specificity=$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	72 mc='$spectrum_matching_parameters.mc'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	73 fixed_mods="$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	74 variable_mods="$spectrum_matching_parameters.variable_mods"
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	75 min_charge=$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	76 max_charge=$spectrum_matching_parameters.max_charge
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	77 fi='$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	78 ri='$spectrum_matching_parameters.ri'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	79 min_isotope='$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	80 max_isotope='$spectrum_matching_parameters.max_isotope'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	81 annotation_level=$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	82 annotation_high_resolution=$spectrum_annotation.annotation_high_resolution
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	83 sequence_index_type=$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	84 sequence_matching_type=$sequence_matching.sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	85 sequence_matching_x=$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	86 import_peptide_length_min=$import_filters.import_peptide_length_min
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	87 import_peptide_length_max=$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	88 import_precursor_mz_ppm=$import_filters.import_precursor_mz_ppm
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	89 exclude_unknown_ptms=$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	90 ptm_score=$ptm_localization.ptm_score
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	91 score_neutral_losses=$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	92 ptm_sequence_matching_type=$ptm_localization.ptm_sequence_matching_type
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	93 ptm_alignment=$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	94 useGeneMapping=$gene_annotation.useGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	95 updateGeneMapping=$gene_annotation.updateGeneMapping
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	96 simplify_groups=$protein_inference.simplify_groups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	97 simplify_score=$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	98 simplify_enzymaticity=$protein_inference.simplify_enzymaticity
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	99 simplify_evidence=$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	100 simplify_uncharacterized=$protein_inference.simplify_uncharacterized
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	101 psm_fdr=$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	102 peptide_fdr=$validation_levels.peptide_fdr
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	103 protein_fdr=$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	104 group_psms=$validation_levels.group_psms
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	105 group_peptides=$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	106 merge_subgroups=$validation_levels.merge_subgroups
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	107 protein_fraction_mw_confidence='$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	108 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	109 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	110 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	111 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	112 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	113 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	114 directag_tic_cutoff=$directag.directag_tic_cutoff
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	115 directag_max_peak_count=$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	116 directag_intensity_classes=$directag.directag_intensity_classes
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	117 directag_adjust_precursor=$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	118 directag_min_adjustment='$directag.directag_min_adjustment'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	119 directag_max_adjustment='$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	120 directag_adjustment_step='$directag.directag_adjustment_step'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	121 directag_charge_states='$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	122 directag_ms_charge_state='$directag.directag_ms_charge_state'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	123 directag_duplicate_spectra='$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	124 directag_deisotoping='$directag.directag_deisotoping'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	125 directag_isotope_tolerance='$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	126 directag_complement_tolerance='$directag.directag_complement_tolerance'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	127 directag_tag_length='$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	128 directag_max_var_mods='$directag.directag_max_var_mods'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	129 directag_max_tag_count='$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	130 directag_intensity_weight='$directag.directag_intensity_weight'
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	131 directag_fidelity_weight='$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	132 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	133 novor_fragmentation=HCD
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	134 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	135 ]]></configfile>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	136 </configfiles>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	137
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	138 <inputs>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	139 <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	140 <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	141 <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	142 <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	143 </param>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	144 <when value="single">
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" 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	146 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	147 <when value="collection">
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	148 <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	149 </when>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	150 </conditional>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	151
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	152 <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	153
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	154 <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	155 <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	156 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	157 <section name="metanovo_parameters" expanded="False" title="MetaNovo Parameters">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	158 <param argument="-mn_specificity" label="Enzyme Specificity" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	159 <option selected="true" value="specific">specific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	160 <option value="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	161 <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	162 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	163 <param argument="-mn_enzymes" label="Enzyme Rule" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	164 <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	165 <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	166 <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	167 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	168 <param argument="-mn_max_missed_cleavages" label="Number of enzymatic missed cleavages" value="2" type="integer" optional="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	169 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	170 <section name="spectrum_matching_parameters" expanded="False" title="Spectrum Matching Parameters">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	171 <param argument="-prec_tol" label="Precursor ion mass tolerance" value="10.0" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	172 <param argument="-prec_ppm" label="Precursor ion tolerance unit" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	173 <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	174 <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	175 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	176 <param argument="-frag_tol" label="Fragment ion mass tolerance" value="0.05" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	177 <param argument="-frag_ppm" label="Fragment ion tolerance unit" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	178 <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	179 <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	180 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	181 <param argument="-digestion" label="Digestion" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	182 <option selected="true" value="0">Enzyme</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	183 <option value="1">Unspecific</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	184 <option value="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	185 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	186 <param argument="-enzyme" label="Enzyme" type="select" multiple="true">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	187 <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	188 <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	189 <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	190 <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	191 <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	192 <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	193 <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	194 <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	195 <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	196 <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	197 <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	198 <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	199 <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	200 <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	201 <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	202 <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	203 <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	204 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	205 <param argument="-specificity" label="Specificity" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	206 <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	207 <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	208 <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	209 <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	210 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	211 <param argument="-mc" label="Number of allowed missed cleavages" value="2" type="text" optional="true" help="If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order, with a comma separated list, e.g. "2, 1"."/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	212 <param argument="-fixed_mods" label="Fixed modifications as comma separated list" type="select" multiple="true">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	213 <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	214 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	215 <param argument="-variable_mods" label="Variable modifications as comma separated list" type="select" multiple="true">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	216 <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	217 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	218 <param argument="-min_charge" label="Minimal charge to search for" value="2" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	219 <param argument="-max_charge" label="Maximal charge to search for" value="4" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	220 <param argument="-fi" label="Type of forward ion searched" value="b" type="text" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	221 <param argument="-ri" label="Type of rewind ion searched" value="y" type="text" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	222 <param argument="-min_isotope" label="Minimum precursor isotope" value="0" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	223 <param argument="-max_isotope" label="Maximum precursor isotope" value="1" type="integer" optional="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	224 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	225 <section name="spectrum_annotation" expanded="False" title="Spectrum Annotation">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	226 <param argument="-annotation_level" label="The intensity threshold to consider for annotation" value="0.75" type="float" optional="true" help="Using percentiles, 0.75 means that the 25% most intense peaks will be annotated."/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	227 <param argument="-annotation_high_resolution" label="If true the most accurate peak will be selected within the m/z tolerance." truevalue="1" falsevalue="0" type="boolean" checked="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	228 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	229 <section name="sequence_matching" expanded="False" title="Sequence Matching">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	230 <param argument="-sequence_index_type" label="sequence_index_type (deprecated)" value="0" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	231 <param argument="-sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	232 <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	233 <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	234 <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	235 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	236 <param argument="-sequence_matching_x" label="The maximal share of Xs in a sequence, 0.25 means 25% of X's" value="0.25" type="float" optional="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	237 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	238 <section name="import_filters" expanded="False" title="Import Filters">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	239 <param argument="-import_peptide_length_min" label="The minimal peptide length to consider when importing identification files" value="8" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	240 <param argument="-import_peptide_length_max" label="The maximal peptide length to consider when importing identification files" value="30" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	241 <param argument="-import_precursor_mz_ppm" label="Maximal precursor ion deviation unit" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	242 <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	243 <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	244 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	245 <param argument="-exclude_unknown_ptms" label="Peptides presenting unrecognized PTMs will be excluded" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	246 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	247 <section name="ptm_localization" expanded="False" title="PTM Localization">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	248 <param argument="-ptm_score" label="The PTM probabilistic score to use for modification localization" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	249 <option value="0">A-score</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	250 <option selected="true" value="1">PhosphoRS</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	251 <option value="2">None</option>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	252 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	253 <param argument="-score_neutral_losses" label="Include neutral losses in spectrum annotation of the PTM score" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	254 <param argument="-ptm_sequence_matching_type" label="The modification to peptide sequence matching type" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	255 <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	256 <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	257 <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	258 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	259 <param argument="-ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	260 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	261 <section name="gene_annotation" expanded="False" title="Gene Annotation">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	262 <param argument="-useGeneMapping" label="Use and save gene mappings along with the project" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	263 <param argument="-updateGeneMapping" label="Update gene mappings automatically from Ensembl" truevalue="1" falsevalue="0" type="boolean" checked="true" help="UniProt databases only"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	264 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	265 <section name="protein_inference" expanded="False" title="Protein Inference">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	266 <param argument="-simplify_groups" label="Simplify protein groups" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	267 <param argument="-simplify_score" label="Simplify protein groups based on the PeptideShaker target/decoy score" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	268 <param argument="-simplify_enzymaticity" label="Simplify protein groups based on the peptide enzymaticity" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	269 <param argument="-simplify_evidence" label="Simplify protein groups based on the UniProt protein evidence" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	270 <param argument="-simplify_uncharacterized" label="Simplify protein groups based on the protein characterization" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	271 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	272 <section name="validation_levels" expanded="False" title="Validation Levels">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	273 <param argument="-psm_fdr" label="FDR at the PSM level in percent" value="1" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	274 <param argument="-peptide_fdr" label="FDR at the peptide level in percent" value="1" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	275 <param argument="-protein_fdr" label="FDR at the protein level in percent" value="1" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	276 <param argument="-group_psms" label="Group PSMs by charge for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	277 <param argument="-group_peptides" label="Group peptides by modification status for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	278 <param argument="-merge_subgroups" label="Merge small PSM and peptide groups for scoring and validation" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
0 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="fraction_analysis" expanded="False" title="Fraction Analysis">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	281 <param argument="-protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="95.0" type="float" optional="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	282 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	283 <section name="directag" expanded="False" title="DirecTag">
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	284 <param argument="-directag_tic_cutoff" label="TIC cutoff in percent" value="85" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	285 <param argument="-directag_max_peak_count" label="Max peak count" value="400" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	286 <param argument="-directag_intensity_classes" label="Number of intensity classes" value="3" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	287 <param argument="-directag_adjust_precursor" label="Adjust precursor" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	288 <param argument="-directag_min_adjustment" label="Minimum precursor adjustment" value="-2.5" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	289 <param argument="-directag_max_adjustment" label="Maximum precursor adjustment" value="2.5" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	290 <param argument="-directag_adjustment_step" label="Precursor adjustment step" value="0.1" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	291 <param argument="-directag_charge_states" label="Number of charge states considered" value="3" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	292 <param argument="-directag_ms_charge_state" label="Use charge state from M spectrum" truevalue="1" falsevalue="0" type="boolean" checked="false"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	293 <param argument="-directag_duplicate_spectra" label="Duplicate spectra per charge" truevalue="1" falsevalue="0" type="boolean" checked="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	294 <param argument="-directag_deisotoping" label="Deisotoping mode" type="select">
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	295 <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	296 <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	297 <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	298 </param>
5 d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	299 <param argument="-directag_isotope_tolerance" label="Isotope mz tolerance" value="0.25" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	300 <param argument="-directag_complement_tolerance" label="Complement mz tolerance" value="0.5" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	301 <param argument="-directag_tag_length" label="Tag length" value="4" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	302 <param argument="-directag_max_var_mods" label="Maximum variable modifications per sequence" value="2" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	303 <param argument="-directag_max_tag_count" label="Maximum tag count" value="5" type="integer" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	304 <param argument="-directag_intensity_weight" label="Intensity score weight" value="1.0" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	305 <param argument="-directag_fidelity_weight" label="Fidelity score weight" value="1.0" type="float" optional="true"/>
d6dcd3173bdf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit fd12c123235f5067858bbd22b70fb0082d1e2199 galaxyp parents: 4 diff changeset	306 <param argument="-directag_complement_weight" label="Complement score weight" value="1.0" type="float" optional="true"/>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	307 </section>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	308 </inputs>
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 <data name="output_fasta" format="fasta" from_work_dir="metanovo/metanovo.fasta" label="${tool.name} on ${on_string}: FASTA"/>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	311 <data name="output_csv" format="csv" from_work_dir="metanovo/metanovo.csv" label="${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	312 </outputs>
4 7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	313 <tests>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	314 <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	315 <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	316 <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	317 <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	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 <!-- Check header. -->
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	320 <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	321 </assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	322 </output>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	323 <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	324 </test>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 </collection>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	332 </param>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	333 <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	334 <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	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 <!-- Check header. -->
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	337 <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	338 </assert_contents>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	339 </output>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	340 <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	341 </test>
7a5ff5359b13 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit c220dc85d59698a73b0f173d46e269e27264d6d8" galaxyp parents: 3 diff changeset	342 </tests>
0 9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	343 <help><![CDATA[
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	344 MetaNovo
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	345
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	346 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	347
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	348 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	349
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	350 - 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	351 - 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	352
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	353 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	354
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	355 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	356
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	357 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	358 Use case Configuration
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	359 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	360 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	361 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	362 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	363 ======================================================= =============
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	364
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	365 \* 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	366
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	367 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	368
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	369 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	370 ]]>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	371 </help>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	372 <citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	373 <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	374 </citations>
9025f297a511 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo commit 97229d4157cf21c8a55433cafdc477d76e0f1c89" galaxyp parents: diff changeset	375 </tool>

Mercurial > repos > galaxyp > metanovo

annotate metanovo.xml @ 5:d6dcd3173bdf draft default tip