diann: diann.xml annotate

annotate diann.xml @ 3:a8f461b7d193 draft default tip

planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25

author	galaxyp
date	Thu, 12 Jun 2025 09:14:41 +0000
parents	65134626eb2b
children

rev	line source
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	2 <description>is a software for DIA/SWATH data processing</description>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	3 <macros>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	4 <token name="@TOOL_VERSION@">1.8.1</token>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	5 <token name="@VERSION_SUFFIX@">5</token>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	6 </macros>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	7 <requirements>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	8 <container type="docker">biocontainers/diann:@TOOL_VERSION@_cv2</container>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	9 </requirements>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	10 <stdio>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	11 <regex source="stdout" match="invalid raw MS data format" level="fatal" description="One of the inputs could not be loaded"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	12 </stdio>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	14 mkdir ./input_data &&
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	15 mkdir ./tmp &&
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	16
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	17 ## generate string like "--f file1 --f file2 ..." for each input in $input.f, which are comma separated
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	18 #set infiles_str = ''
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	19 #for $infile in $input.f
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	20 #if not $infile:
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	21 #continue
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	22 #end if
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	23 ## if brukertdf.d.tar, extract to ./input_data and append "./input_data/" to infiles_str
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	24 #if $infile.is_of_type("brukertdf.d.tar"):
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	25 tar -xf '$infile' -C ./input_data &&
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	26 #set $infiles_str += "--f './input_data/" + str($infile.element_identifier[:-4]) + "' "
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	27 #else
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	28 #set name = './input_data/' + $infile.element_identifier + '.' + $infile.ext
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	29 ln -s '$infile' '$name' &&
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	30 #set $infiles_str += "--f '" + $name + "' "
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	31 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	32 #end for
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	33
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	34 #set $fasta_file_str = ''
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	35 #for $fasta_file in $input.fasta_db_options.fasta
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	36 #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	37 #end for
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	38
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	39 #if $input.spectral_lib_options.lib
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	40 ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' &&
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	41 #end if
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	42
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	43 diann
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	44 #if $infiles_str != ''
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	45 $infiles_str
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	46 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	47 --dir ./
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	48 #if $input.spectral_lib_options.lib
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	49 --lib './input_data/report-lib.predicted.speclib'
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	50 #else
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	51 --lib
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	52 #end if
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	53 #if $infiles_str != ''
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	54 --out ./report.tsv
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	55 #end if
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	56 #if $input.spectral_lib_options.gen_spec_lib
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	57 --out-lib ./report-lib.tsv
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	58 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	59 --threads \${GALAXY_SLOTS:-1}
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	60 --temp ./tmp
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	61
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	62 ## Spectral library options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	63 $input.spectral_lib_options.gen_spec_lib
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	64 #if $input.spectral_lib_options.library_headers
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	65 --library-headers '$input.spectral_lib_options.library_headers'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	66 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	67 $input.spectral_lib_options.no_lib_filter
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	68 #if $input.spectral_lib_options.learn_lib
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	69 --learn-lib '$input.spectral_lib_options.learn_lib'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	70 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	71 $input.spectral_lib_options.out_measured_rt
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	72 $input.spectral_lib_options.predictor
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	73 $input.spectral_lib_options.reannotate
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	74 ##if $input.spectral_lib_options.ref
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	75 ##--ref '$input.spectral_lib_options.ref'
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	76 ###end if
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	77
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	78 ## FASTA database options
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	79 #if $fasta_file_str != '--fasta None '
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	80 '$fasta_file_str'
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	81 #end if
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	82 #if $input.fasta_db_options.fasta_filter
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	83 --fasta-filter '$input.fasta_db_options.fasta_filter'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	84 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	85 $input.fasta_db_options.fasta_search
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	86
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	87 ## Algorithm options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	88 $algo_options.no_calibration
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	89 #if $algo_options.mass_acc
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	90 --mass-acc '$algo_options.mass_acc'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	91 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	92 #if $algo_options.mass_acc_cal
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	93 --mass-acc-cal '$algo_options.mass_acc_cal'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	94 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	95 #if $algo_options.mass_acc_ms1
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	96 --mass-acc-ms1 '$algo_options.mass_acc_ms1'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	97 #end if
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	98 ##$algo_options.quick_mass_acc
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	99 $algo_options.reanalyse
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	100 $algo_options.mbr_fix_settings
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	101 $algo_options.relaxed_prot_inf
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	102 $algo_options.prot_inf
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	103 $algo_options.nn_classifier
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	104 $algo_options.quant_strategy
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	105 $algo_options.cross_run_norm
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	106 $algo_options.lib_gen_strategy
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	107
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	108 ## Ion mobility options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	109 ## ToDo: no_im_window as condition?
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	110 $im_window_options.no_im_window
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	111 #if $im_window_options.window
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	112 --window '$im_window_options.window'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	113 --im-window '$im_window_options.im_window'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	114 --im-window-factor '$im_window_options.im_window_factor'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	115 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	116
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	117 ## Precursor options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	118 --cut '$precursor_options.cleavage_spec.cut'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	119 --missed-cleavages '$precursor_options.missed_cleavages'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	120 $precursor_options.met_excision
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	121 --min-pep-len '$precursor_options.min_pep_len'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	122 --max-pep-len '$precursor_options.max_pep_len'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	123 --min-pr-mz '$precursor_options.min_pr_mz'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	124 --max-pr-mz '$precursor_options.max_pr_mz'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	125 --min-pr-charge '$precursor_options.min_pr_charge'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	126 --max-pr-charge '$precursor_options.max_pr_charge'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	127 --min-fr-mz '$precursor_options.min_fr_mz'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	128 --max-fr-mz '$precursor_options.max_fr_mz'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	129 $precursor_options.nn_single_seq
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	130 #if $precursor_options.int_removal
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	131 --int-removal '$precursor_options.int_removal'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	132 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	133
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	134 ## Fragment options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	135 $mass_frag_options.no_fr_selection
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	136 #if $mass_frag_options.quant_fr
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	137 --quant-fr '$mass_frag_options.quant_fr'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	138 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	139 $mass_frag_options.restrict_fr
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	140 #if $mass_frag_options.sptxt_acc
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	141 --sptxt-acc '$mass_frag_options.sptxt_acc'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	142 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	143 #if $mass_frag_options.target_fr
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	144 --target-fr '$mass_frag_options.target_fr'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	145 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	146
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	147 ## Channel options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	148 ## ToDo: no_decoy_channel as condition?
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	149 ##if $channel_options.channels
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	150 ##--channels '$channel_options.channels'
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	151 ###end if
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	152 #if $channel_options.decoy_channel
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	153 --decoy-channel '$channel_options.decoy_channel'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	154 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	155 $channel_options.no_decoy_channel
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	156
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	157 ## Modification options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	158 #if $mod_options.fixed_mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	159 --fixed-mod '$mod_options.fixed_mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	160 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	161 #if $mod_options.var_mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	162 --var-mod '$mod_options.var_mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	163 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	164 #if $mod_options.var_mods
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	165 --var-mods '$mod_options.var_mods'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	166 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	167 #if $mod_options.mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	168 --mod '$mod_options.mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	169 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	170 #if $mod_options.monitor_mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	171 --monitor-mod '$mod_options.monitor_mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	172 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	173 #if $mod_options.no_cut_after_mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	174 --no-cut-after-mod '$mod_options.no_cut_after_mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	175 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	176 $mod_options.original_mods
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	177 $mod_options.clear_mods
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	178 #if $mod_options.lib_fixed_mod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	179 --lib-fixed-mod '$mod_options.lib_fixed_mod'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	180 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	181 $mod_options.mod_only
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	182 $mod_options.strip_unknown_mods
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	183 $mod_options.unimod4
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	184 $mod_options.unimod35
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	185
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	186 ## Quantification options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	187 $quantification_options.peak_translation
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	188 $quantification_options.no_maxlfq
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	189
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	190 ## Other options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	191 #if $other_options.min_peak
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	192 --min-peak '$other_options.min_peak'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	193 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	194 $other_options.no_rt_window
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	195 $other_options.no_stratification
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	196 $other_options.no_swissprot
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	197 $other_options.dl_no_im
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	198 $other_options.dl_no_rt
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	199 $other_options.duplicate_proteins
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	200 $other_options.exact_fdr
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	201 $other_options.force_swissprot
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	202 $other_options.full_unimod
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	203 $other_options.gen_fr_restriction
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	204 $other_options.global_mass_cal
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	205 ##$other_options.il_eq
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	206 $other_options.individual_mass_acc
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	207 $other_options.individual_reports
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	208 $other_options.individual_windows
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	209 $other_options.no_isotopes
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	210 $other_options.regular_swath
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	211 $other_options.scanning_swath
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	212 ##$other_options.semi
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	213 $other_options.species_genes
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	214 $other_options.tims_skip_errors
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	215
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	216 ## Output options
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	217 $output_options.no_main_report
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	218 $output_options.no_stats
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	219 $output_options.compact_report
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	220 $output_options.matrices
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	221 #if $output_options.matrix_ch_qvalue
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	222 --matrix-ch-qvalue '$output_options.matrix_ch_qvalue'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	223 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	224 --qvalue $output_options.qvalue
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	225 #if $output_options.matrix_tr_qvalue
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	226 --matrix-tr-qvalue '$output_options.matrix_tr_qvalue'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	227 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	228 $output_options.matrix_spec_q
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	229 $output_options.report_lib_info
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	230 #if $output_options.vis
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	231 --vis '$output_options.vis'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	232 #end if
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	233 --verbose '$output_options.verbose'
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	234 ]]></command>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	235 <inputs>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	236 <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	237 <section name="input" expanded="true" title="Input files">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	238 <param name="f" type="data" format="mzml,wiff,thermo.raw,brukertdf.d.tar" multiple="true" optional="true" label="Input file" help="Specify a run to be analysed"/>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	239 <!-- ToDo lib: The use of multiple lib commands (experimental) allows to load multiple libraries in .tsv format -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	240 <section name="spectral_lib_options" title="Spectral library">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	241 <param name="gen_spec_lib" type="boolean" truevalue="--gen-spec-lib" falsevalue="" checked="false" label="Generate a spectral library" help="Instructs DIA-NN to generate a spectral library"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	242 <param name="predictor" type="boolean" truevalue="--predictor" falsevalue="" checked="false" label="Perform deep learning-based prediction of spectra, retention times and ion mobility values" help="Instructs DIA-NN to perform deep learning-based prediction of spectra, retention times and ion mobility values"/>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	243 <!-- Removed sptxt,msp as input format > experimental feature-->
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	244 <param name="lib" type="data" format="csv,tsv,xls,txt,binary" optional="true" label="Spectral library" help="Specify a spectral library"/>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	245 <param name="library_headers" type="text" optional="true" label="Library headers" help="Specifies column names in the spectral library to be used, in the order described in Spectral library formats [name 1],[name 2],.... Use '*' instead of the column name if DIA-NN already recognizes its name"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	246 <param name="no_lib_filter" type="boolean" truevalue="--no-lib-filter" falsevalue="" checked="false" label="Use the input library 'as is'" help="The input library will be used 'as is' without discarding fragments that might be harmful for the analysis; use with caution"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	247 <param name="learn_lib" type="data" format="tsv" optional="true" label="Training library" help="Specifies a 'training library' for the legacy predictor"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	248 <param name="out_measured_rt" type="boolean" truevalue="--out-measured-rt" falsevalue="" checked="false" label="Save raw empirical retention times in the spectral library" help="Instructs DIA-NN to save raw empirical retention times in the spectral library being generated, instead of saving RTs aligned to a particular scale"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	249 <param name="reannotate" type="boolean" truevalue="--reannotate" falsevalue="" checked="false" label="Reannotate the spectral library with protein information from the FASTA database" help="Reannotate the spectral library with protein information from the FASTA database, using the specified digest specificity"/>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	250 <!-- <param name="ref" type="text" optional="true" label="Reference run" help="(Experimental) Specify a special (small) spectral library which will be used exclusively for calibration - this function can speed up calibration in library-free searches"/>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	251 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	252 <section name="fasta_db_options" title="FASTA database">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	253 <param name="fasta" type="data" format="fasta" optional="true" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	254 <param name="fasta_filter" type="data" format="txt" optional="true" label="Fasta filter" help="Only consider peptides matching the stripped sequences specified in the text file provided, when processing a sequence database"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	255 <param name="fasta_search" type="boolean" truevalue="--fasta-search" falsevalue="" checked="false" label="Perform in silico digest of the sequence database" help="Instructs DIA-NN to perform an in silico digest of the sequence database"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	256 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	257 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	258 <section name="algo_options" title="Algorithm">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	259 <param name="no_calibration" type="boolean" truevalue="--no-calibration" falsevalue="" checked="false" label="Disable mass calibration" help="Disables mass calibration"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	260 <param name="mass_acc" type="float" min="0" optional="true" label="MS2 mass accuracy" help="Sets the MS2 mass accuracy to N ppm"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	261 <param name="mass_acc_cal" type="float" min="0" optional="true" label="Mass accuracy during calibration phase" help="Sets the mass accuracy used during the calibration phase of the search to N ppm"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	262 <param name="mass_acc_ms1" type="float" min="0" optional="true" label="MS1 mass accuracy" help="Sets the MS1 mass accuracy to N ppm"/>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	263 <!-- <param name="quick_mass_acc" type="boolean" truevalue="--quick-mass-acc" falsevalue="" checked="false" label="(Experimental) Use a fast heuristical algorithm for MS2 mass accuracy" help="When choosing the MS2 mass accuracy setting automatically, DIA-NN will use a fast heuristical algorithm instead of IDs number optimisation"/>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	264 <!-- ToDo mbr_fix_settings: what does 'Unrelated runs' mean? -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	265 <param name="reanalyse" type="boolean" truevalue="--reanalyse" falsevalue="" checked="false" label="Enable MBR" help="Enables MBR"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	266 <param name="mbr_fix_settings" type="boolean" truevalue="--mbr-fix-settings" falsevalue="" checked="false" label="Use the same settings for all runs during the second MBR pass" help="When using the 'Unrelated runs' option in combination with MBR, the same settings will be used to process all runs during the second MBR pass"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	267 <param name="relaxed_prot_inf" type="boolean" truevalue="--relaxed-prot-inf" falsevalue="" checked="true" label="Use a very heuristical protein inference algorithm" help="Instructs DIA-NN to use a very heuristical protein inference algorithm (similar to the one used by FragPipe and many other software tools), wherein DIA-NN aims to make sure that no protein is present simultaneously in multiple protein groups. This mode (i) is recommended for method optimisation and benchmarks, (ii) might be convenient for gene set enrichment analysis and related kinds of downstream processing. However the alternative protein inference strategy of DIA-NN is more reliable for differential expression analyses (this is one of the advantages of DIA-NN). Equivalent to the 'Heuristic protein inference' GUI setting."/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	268 <param name="prot_inf" type="select" label="Protein inference" help="Controls the protein inference mode. If protein inference (that is protein grouping) is disabled, protein groups from the spectral library will be used instead">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	269 <option value="--pg-level 0">Isoform IDs</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	270 <option value="--pg-level 1">Protein names (from FASTA)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	271 <option value="--pg-level 2">Genes (species-specific)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	272 <option value="" selected="True">Genes</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	273 <option value="--no-prot-inf">Off</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	274 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	275 <param name="nn_classifier" type="select" label="Neural network classifier" help="Activates the neural network classifier. Default is single-pass mode. Double-pass mode is the best in most cases but is about twice slower than single-pass">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	276 <option value="" selected="True">Single-pass mode</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	277 <option value="--double-search">Double-pass mode</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	278 <option value="--no-nn">off</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	279 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	280 <param name="quant_strategy" type="select" label="Quantification strategy" help="Quantification algorithms. --no-ifs-removal/Any LC (high precision): Turns off interference subtraction from fragment ion chromatograms. --peak-center/Robust LC (high accuracy): Instructs DIA-NN to integrate chromatographic peaks only in the vicinity of the apex. Robust LC (high precision): combination of --peak-center and --no-ifs-removal. --peak-height/Peak-height Instructs DIA-NN to use the apex height of the peak for quantification - equivalent to the 'Peak height' quantification mode.">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	281 <option value="">Any LC (high accuracy)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	282 <option value="--no-ifs-removal">Any LC (high precision)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	283 <option value="--peak-center">Robust LC (high accuracy)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	284 <option value="--peak-center --no-ifs-removal" selected="True">Robust LC (high precision)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	285 <option value="--peak-height">Peak-height</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	286 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	287 <param name="cross_run_norm" type="select" label="Cross-run normalisation" help="Normalisation strategy. --global-norm/Global: Instructs DIA-NN to use simple global normalisation instead of RT-dependent normalisation. RT-dependent: Instructs DIA-NN to use RT-dependent normalisation. --sig-norm/RT and signal-dep. (experimental): Instructs DIA-NN to use RT and signal dependent normalisation (experimental). --no-norm/Off: disables cross-run normalisation. Normalised quantities reported along with the raw quantities. Default: RT-dependent">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	288 <option value="--global-norm">Global</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	289 <option value="" selected="True">RT-dependent</option>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	290 <!-- <option value="--sig-norm">RT and signal-dep. (experimental)</option>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	291 <option value="--no-norm">Off</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	292 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	293 <param name="lib_gen_strategy" type="select" label="Library generationm strategy" help="Enables an intelligent algorithm which determines how to extract spectra, when creating a spectral library from DIA data. This is highly recommended and should almost always be enabled">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	294 <option value="--id-profiling">IDs profiling</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	295 <option value="--rt-profiling">IDs, RT and IM profiling</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	296 <option value="--smart-profiling" selected="true">Smart profiling</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	297 <option value="">Full profiling</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	298 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	299 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	300 <section name="im_window_options" title="Ion mobility window">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	301 <param name="no_im_window" type="boolean" truevalue="--no-im-window" falsevalue="" checked="false" label="Disable IM-windowed search" help="Disables IM-windowed search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	302 <param name="window" type="integer" min="0" optional="true" label="Scan window radius" help="Sets the scan window radius to a specific value. Ideally, should be approximately equal to the average number of data points per peak"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	303 <param name="im_window" type="integer" min="0" optional="true" label="IM extraction window" help="Fixes IM extraction window to the specific value"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	304 <param name="im_window_factor" type="float" min="0" value="2.0" label="IM extraction window factor" help="Controls the minimum size of the IM extraction window. Default is 2.0"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	305 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	306 <section name="precursor_options" title="Precursor ion generation">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	307 <conditional name="cleavage_spec">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	308 <param name="cut_type" type="select" label="Cleavage specificity">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	309 <option value="predefined">Predefined cleavage pattern</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	310 <option value="own">Define your own cleavage pattern</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	311 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	312 <when value="predefined">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	313 <param name="cut" type="select" label="Protease" help="Specifies cleavage specificity for the in silico digest. Cleavage sites (pairs of amino acids) are listed separated by commas, '' indicates any amino acid, and '!' indicates that the respective site will not be cleaved. Examples: K,R,!P - canonical tryptic specificity, leave blank to disable digest">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	314 <option value="K,R" selected="true">Trypsin/P</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	315 <option value="K,R,!P">Trypsin (excluding cuts at P)</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	316 <option value="K*">Lys-C</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	317 <option value="F,Y,W,M,L,!P">Chymotrypsin</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	318 <option value="*D">AspN</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	319 <option value="E*">GluC</option>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	320 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	321 </when>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	322 <when value="own">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	323 <param name="cut" type="text" label="Cleavage pattern" help="Cleavage sites (pairs of amino acids) are listed separated by commas, '' indicates any amino acid, and '!' indicates that the respective site will not be cleaved. For example: K,R,!P for canonical tryptic specificity.">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	324 </param>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	325 </when>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	326 </conditional>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	327 <param name="missed_cleavages" type="integer" min="0" max="5" value="1" label="Maximum number of missed cleavages" help="Sets the maximum number of missed cleavages"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	328 <param name="met_excision" type="boolean" truevalue="--met-excision" falsevalue="" checked="true" label="Enable protein N-term methionine excision" help="Enables protein N-term methionine excision as variable modification for the in silico digest"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	329 <param name="min_pep_len" type="integer" min="5" max="100" value="7" label="Minimum precursor length" help="Sets the minimum precursor length for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	330 <param name="max_pep_len" type="integer" min="5" max="100" value="30" label="Maximum precursor length" help="Sets the maximum precursor length for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	331 <param name="min_pr_mz" type="integer" min="0" value="300" label="Minimum precursor m/z" help="Sets the minimum precursor m/z for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	332 <param name="max_pr_mz" type="integer" min="0" value="1800" label="Maximum precursor m/z" help="Sets the maximum precursor m/z for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	333 <param name="min_pr_charge" type="integer" min="1" max="10" value="1" optional="true" label="Minimum precursor charge" help="Sets the minimum precursor charge for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	334 <param name="max_pr_charge" type="integer" min="0" max="10" value="4" label="Maximum precursor charge" help="Sets the maximum precursor charge for the in silico library generation or library-free search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	335 <param name="min_fr_mz" type="integer" min="0" value="200" label="Minimum number of fragments per precursors" help="Specifies the minimum number of fragments per precursors in the spectral library being saved"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	336 <param name="max_fr_mz" type="integer" min="0" value="1800" label="Maximum fragments per precursor" help="Specifies the maximum number of fragments per precursor in the spectral library being saved"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	337 <param name="nn_single_seq" type="boolean" truevalue="--nn-single-seq" falsevalue="" checked="false" label="Use one precursor per stripped sequence for training" help="Only use one (best) precursor per stripped sequence for the training of the neural network classifier"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	338 <param name="int_removal" type="integer" min="0" optional="true" label="Interference removal" help="Specify 0 to disable the removal of interfering precursors"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	339 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	340 <section name="mod_options" title="Modifications">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	341 <param name="fixed_mod" type="text" optional="true" label="Fixed modification" help="Adds the modification name to the list of recognised names and specifies the modification as fixed [name],[mass],[sites],[optional: 'label']"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	342 <param name="var_mod" type="text" optional="true" label="Variable modification" help="Adds the modification name to the list of recognised names and specifies the modification as variable [name],[mass],[sites],[optional: 'label']. [sites] can contain a list of amino acids and 'n' which codes for the N-terminus of the peptide. 'n' indicates protein N-terminus. Similar to --mod can be followed by 'label' Examples: UniMod:21,79.966331,STY - phosphorylation, UniMod:1,42.010565,n - N-terminal protein acetylation." />
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	343 <param name="var_mods" type="integer" min="0" optional="true" label="Maximum number of variable modifications" help="Sets the maximum number of variable modifications"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	344 <param name="mod" type="text" optional="true" label="Modification name" help="Declares a modification name [name],[mass],[optional: 'label']. Examples: UniMod:5,43.005814, SILAC-Lys8,8.014199,label"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	345 <!-- ToDo monitor_mod: This modification must have been declared as variable using var-mod -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	346 <param name="monitor_mod" type="text" optional="true" label="Modification for PTM scoring and site localisation" help="Apply PTM scoring and site localisation for a particular modification"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	347 <param name="no_cut_after_mod" type="text" optional="true" label="No cut after modification" help="Discard peptides generated via in silico cuts after residues bearing a particular modification. Example: SILAC-Lys8"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	348 <param name="original_mods" type="boolean" truevalue="--original-mods" falsevalue="" checked="false" label="Disable automatic conversion of known modifications" help="Disables the automatic conversion of known modifications to the UniMod format names"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	349 <param name="clear_mods" type="boolean" truevalue="--clear-mods" falsevalue="" checked="false" label="Clear modifications" help="Makes DIA-NN 'forget' all built-in modification (PTM) names"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	350 <param name="lib_fixed_mod" type="text" label="In silico modification" help="Applies a modification, previously declared using --fixed-mod, to a spectral library"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	351 <param name="mod_only" type="boolean" truevalue="--mod-only" falsevalue="" checked="false" label="Only consider peptides bearing the modifications listed" help="Only consider peptides bearing the modifications listed with --monitor-mod"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	352 <param name="strip_unknown_mods" type="boolean" truevalue="--strip-unknown-mods" falsevalue="" checked="false" label="Ignore modifications not supported by the deep learning predictor" help="Instructs DIA-NN to ignore modifications that are not supported by the deep learning predictor, when performing the prediction"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	353 <param name="unimod4" type="boolean" truevalue="--unimod4" falsevalue="" checked="true" label="Considers C carbamidomethylation" help=""/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	354 <param name="unimod35" type="boolean" truevalue="--unimod35" falsevalue="" checked="false" label="Considers Ox(M) methionine oxidation" help=""/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	355 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	356 <section name="mass_frag_options" title="Mass calibration and Fragmentation">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	357 <param name="no_fr_selection" type="boolean" truevalue="--no-fr-selection" falsevalue="" checked="false" label="Disable selection of fragments for quantification" help="The selection of fragments for quantification based on the quality assessment of the respective extracted chromatograms will be disabled"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	358 <param name="quant_fr" type="integer" min="0" optional="true" label="Number of top fragment ions for quantification" help="Sets the number of top fragment ions among which the fragments that will be used for quantification are chosen. Default value is 6"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	359 <param name="restrict_fr" type="boolean" truevalue="--restrict-fr" falsevalue="" checked="false" label="Restrict fragments for quantification" help="Some fragments will not be used for quantification, based on the value in the ExcludeFromAssay spectral library column"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	360 <param name="sptxt_acc" type="integer" min="0" optional="true" label="Fragment filtering mass accuracy" help="Sets the fragment filtering mass accuracy (in ppm) when reading .sptxt/.msp libraries"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	361 <param name="target_fr" type="integer" min="0" optional="true" label="Number of fragment ions for spectral library" help="Fragment ions beyond this number will only be included in the spectral library being created (from DIA data) if they have high-quality chromatograms. Default value is 6"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	362 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	363 <section name="channel_options" title="Channel">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	364 <!-- <param name="channels" type="text" optional="true" label="(Experimental) List multiplexing channels" help="Lists multiplexing channels, wherein each channel declaration has the form [channel] = [label group],[channel name],[sites],[mass1:mass2:...], wherein [sites] has the same syntax as for --var-mod and if N sites are listed, N masses are listed at the end of the channel declaration. Examples: '--channels SILAC,L,KR,0:0; SILAC,H,KR,8.014199:10.008269' - declares standard light/heavy SILAC labels, '--channels mTRAQ,0,nK,0:0; mTRAQ,4,nK,4.0070994:4.0070994;mTRAQ,8,nK,8.0141988132:8.0141988132' - declares mTRAQ. The spectral library will be automatically split into multiple channels, for precursors bearing the [label group] modification. To add the latter to a label-free spectral library, can use --lib-fixed-mod, e.g. --fixed-mod SILAC,0.0,KR,label --lib-fixed-mod SILAC. The --channels command must be used in conjunction with --peak-translation."/>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	365 <param name="decoy_channel" type="text" optional="true" label="Decoy channel" help="Specifies the decoy channel masses (same syntax as for --channels)"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	366 <param name="no_decoy_channel" type="boolean" truevalue="--no-decoy-channel" falsevalue="" checked="false" label="Disable the use of a decoy channel" help="Disables the use of a decoy channel for channel q-value calculation"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	367 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	368 <section name="quantification_options" title="Quantification">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	369 <param name="peak_translation" type="boolean" truevalue="--peak-translation" falsevalue="" checked="false" label="Take advantage of the co-elution of isotopologues" help="Instructs DIA-NN to take advantage of the co-elution of isotopologues, when identifying and quantifying precursors"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	370 <param name="no_maxlfq" type="boolean" truevalue="--no-maxlfq" falsevalue="" checked="false" label="Disable MaxLFQ for protein quantification" help="Disables MaxLFQ for protein quantification"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	371 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	372 <section name="other_options" title="Other">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	373 <param name="min_peak" type="float" min="0.01" optional="true" label="Minimum peak height" help="Sets the minimum peak height to consider"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	374 <param name="no_rt_window" type="boolean" truevalue="--no-rt-window" falsevalue="" checked="false" label="Disable RT-windowed search" help="Disables RT-windowed search"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	375 <param name="no_stratification" type="boolean" truevalue="--no-stratification" falsevalue="" checked="false" label="Disable precursor stratification" help="Disables precursor stratification based on the modification status. Stratification works in combination with monitor-mod to ensure that no matter how few modified peptides are reported, the FDR specifically across modified peptides is well controlled."/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	376 <param name="no_swissprot" type="boolean" truevalue="--no-swissprot" falsevalue="" checked="false" label="Do not give preference for SwissProt proteins" help="Instruct DIA-NN not to give preference for SwissProt proteins when inferring protein groups"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	377 <param name="dl_no_im" type="boolean" truevalue="--dl-no-im" falsevalue="" checked="false" label="Disable ion mobility prediction" help="When using the deep learning predictor, prediction of ion mobilities will not be performed"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	378 <param name="dl_no_rt" type="boolean" truevalue="--dl-no-rt" falsevalue="" checked="false" label="Disable retention time prediction" help="When using the deep learning predictor, prediction of retention times will not be performed"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	379 <param name="duplicate_proteins" type="boolean" truevalue="--duplicate-proteins" falsevalue="" checked="false" label="Duplicate proteins" help="Instructs DIA-NN not to skip entries in the sequence database with duplicate IDs (while by default if several entries have the same protein ID, all but the first entry will be skipped)"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	380 <param name="exact_fdr" type="boolean" truevalue="--exact-fdr" falsevalue="" checked="false" label="Disable approximate FDR estimation" help="Approximate FDR estimation for confident peptides based on parametric modelling will be disabled"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	381 <param name="force_swissprot" type="boolean" truevalue="--force-swissprot" falsevalue="" checked="false" label="Force SwissProt sequences" help="Only consider SwissProt sequences when processing a sequence database"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	382 <param name="full_unimod" type="boolean" truevalue="--full-unimod" falsevalue="" checked="false" label="Full UniMod modification database" help="Loads the complete UniMod modification database and disables the automatic conversion of modification names to the UniMod format"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	383 <param name="gen_fr_restriction" type="boolean" truevalue="--gen-fr-restriction" falsevalue="" checked="false" label="Generate fragment exclusion information" help="Annotates the library with fragment exclusion information, based on the runs being analysed (fragments least affected by interferences are selected for quantification, why the rest are excluded)"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	384 <param name="global_mass_cal" type="boolean" truevalue="--global-mass-cal" falsevalue="" checked="false" label="Disable RT-dependent mass calibration" help="Disables RT-dependent mass calibration"/>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	385 <!-- <param name="il_eq" type="boolean" truevalue="--il-eq" falsevalue="" checked="false" label="(Experimental) Isoleucine and leucine equivalent" help="When using the 'Reannotate' function, peptides will be matched to proteins while considering isoleucine and leucine equivalent"/>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	386 <!-- ToDo individual_mass_acc: what does automatic mean? -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	387 <param name="individual_mass_acc" type="boolean" truevalue="--individual-mass-acc" falsevalue="" checked="false" label="Independent mass accuracies" help="Mass accuracies, if set to automatic, will be determined independently for different runs"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	388 <param name="individual_reports" type="boolean" truevalue="--individual-reports" falsevalue="" checked="false" label="Individual output reports" help="A separate output report will be created for each run"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	389 <!-- ToDo individual_windows: what does automatic mean? -->
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	390 <param name="individual_windows" type="boolean" truevalue="--individual-windows" falsevalue="" checked="false" label="Independent scan windows" help="Scan window, if set to automatic, will be determined independently for different runs"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	391 <param name="no_isotopes" type="boolean" truevalue="--no-isotopes" falsevalue="" checked="false" label="Do not extract chromatograms for heavy isotopologues" help="Do not extract chromatograms for heavy isotopologues"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	392 <param name="regular_swath" type="boolean" truevalue="--regular-swath" falsevalue="" checked="false" label="Analyse all runs as regular runs" help="All runs will be analysed as if they were not Scanning SWATH runs"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	393 <param name="scanning_swath" type="boolean" truevalue="--scanning-swath" falsevalue="" checked="false" label="Analyse all runs as Scanning SWATH runs" help="All runs will be analysed as if they were Scanning SWATH runs"/>
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	394 <!-- <param name="semi" type="boolean" truevalue="--semi" falsevalue="" checked="false" label="(Experimental) Match a peptide to a protein with one specific and one non-specific cut" help="When using the 'Reannotate' function, a peptide will be matched to a protein also if it could be obtained with one specific and one non-specific cut (at either of the termini)"/>-->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	395 <param name="species_genes" type="boolean" truevalue="--species-genes" falsevalue="" checked="false" label="Add the organism identifier to the gene names" help="Instructs DIA-NN to add the organism identifier to the gene names - useful for distinguishing genes from different species, when analysing mixed samples. Works with UniProt sequence databases."/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	396 <param name="tims_skip_errors" type="boolean" truevalue="--tims-skip-errors" falsevalue="" checked="false" label="Ignore errors when loading dia-PASEF data" help="DIA-NN will ignore errors when loading dia-PASEF data"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	397 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	398 <section name="output_options" expanded="true" title="Output">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	399 <param name="no_main_report" type="boolean" truevalue="--no-main-report" falsevalue="" checked="false" label="Do not produce the main report" help="Do not produce the main report"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	400 <param name="no_stats" type="boolean" truevalue="--no-stats" falsevalue="" checked="false" label="Disable generation of the stats file" help="Disables the generation of the stats file"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	401 <param name="compact_report" type="boolean" truevalue="--compact-report" falsevalue="" checked="false" label="Compact report" help="Instructs DIA-NN to provide less information in the main report"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	402 <param name="matrices" type="boolean" truevalue="--matrices" falsevalue="" checked="true" label="Output quantities matrices" help="Outputs quantities matrices"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	403 <param name="matrix_ch_qvalue" type="float" min="0" optional="true" label="Channel q-value" help="Sets the 'channel q-value' used to filter the output matrices"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	404 <param name="qvalue" type="float" min="0" value="0.01" label="q-value" help="Sets the q-value used to filter the output matrices"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	405 <param name="matrix_tr_qvalue" type="float" min="0" optional="true" label="Translated q-value" help="Sets the 'translated q-value' used to filter the output matrices"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	406 <param name="matrix_spec_q" type="boolean" truevalue="--matrix-spec-q" falsevalue="" checked="false" label="Run-specific protein q-value filtering" help="Run-specific protein q-value filtering will be used when saving protein matrices. The ability to filter based on run-specific protein q-values, which allows to generate highly reliable data, is one of the advantages of DIA-NN."/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	407 <param name="report_lib_info" type="boolean" truevalue="--report-lib-info" falsevalue="" checked="false" label="Add extra library information to the main output report" help="Adds extra library information on the precursor and its fragments to the main output report"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	408 <param name="vis" type="text" optional="true" label="Extract and save chromatograms" help="Instructs DIA-NN to extract and save chromatograms in the vicinity of the detected elution apex, for all PSMs matching the stripped sequences provided, for all runs in the experiment; at least N scans in the vicinity of the apex will be extracted"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	409 <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	410 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	411 </inputs>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	412 <outputs>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	413 <data format="tabular" name="output_report" from_work_dir="report.tsv" label="${tool.name} on ${on_string}: report.tsv">
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	414 <filter>input['f'] != None</filter>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	415 </data>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	416 <data format="tabular" name="output_report_lib" from_work_dir="report-lib.tsv" label="${tool.name} on ${on_string}: report-lib.tsv">
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	417 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	418 <filter>input['f'] != None</filter>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	419 </data>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	420 <data format="data" name="output_report_speclib" from_work_dir="report-lib.tsv.speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib">
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	421 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	422 <filter>input['f'] != None</filter>
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	423 </data>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	424 <data format="data" name="output_report_pred_speclib" from_work_dir="report-lib.predicted.speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib">
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	425 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	426 </data>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	427 </outputs>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	428 <tests>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	429 <!-- test for default run -->
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	430 <test expect_num_outputs="4">
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	431 <section name="input">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	432 <param name="f" value="small-peakpicking-cwt-allMS" />
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	433 <section name="spectral_lib_options">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	434 <param name="gen_spec_lib" value="True"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	435 <param name="predictor" value="True"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	436 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	437 <section name="fasta_db_options">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	438 <param name="fasta" value="bsa.fasta"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	439 <param name="fasta_search" value="True"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	440 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	441 </section>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	442 <output name="output_report" file="report.tsv">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	443 <assert_contents>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	444 <has_text text="PG.Normalised"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	445 </assert_contents>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	446 </output>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	447 <output name="output_report_lib" file="report-lib.tsv">
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	448 <assert_contents>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	449 <has_text text="PrecursorMz"/>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	450 </assert_contents>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	451 </output>
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	452 <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	453 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	454 </test>
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	455 <!-- test for default run wo MS files -->
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	456 <test expect_num_outputs="1">
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	457 <section name="input">
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	458 <section name="spectral_lib_options">
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	459 <param name="gen_spec_lib" value="True"/>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	460 <param name="predictor" value="True"/>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	461 </section>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	462 <section name="fasta_db_options">
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	463 <param name="fasta" value="bsa.fasta"/>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	464 <param name="fasta_search" value="True"/>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	465 </section>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	466 </section>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	467 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	468 </test>
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	469 <!-- test for multiple fastas -->
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	470 <test expect_num_outputs="1">
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	471 <section name="input">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	472 <param name="f" value="small-peakpicking-cwt-allMS" />
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	473 <section name="fasta_db_options">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	474 <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	475 <param name="fasta_search" value="True"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	476 </section>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	477 </section>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	478 <output name="output_report" file="report.tsv">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	479 <assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	480 <has_text text="PG.Normalised"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	481 </assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	482 </output>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	483 </test>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	484 <!-- test for spec library -->
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	485 <test expect_num_outputs="1">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	486 <section name="input">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	487 <param name="f" value="small-peakpicking-cwt-allMS" />
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	488 <section name="spectral_lib_options">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	489 <param name="lib" value="report-lib.predicted.speclib"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	490 </section>
1 c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	491 <section name="fasta_db_options">
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	492 <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	493 <param name="fasta_search" value="True"/>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	494 </section>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	495 </section>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	496 <output name="output_report" file="report.tsv">
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	497 <assert_contents>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	498 <has_text text="PG.Normalised"/>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	499 </assert_contents>
c9228a392c74 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	500 </output>
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	501 </test>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	502 <!-- test for Bruker data -->
3 a8f461b7d193 planemo upload for repository https://github.com/vdemichev/DiaNN commit 7066fc6839300c6703770e667f8534ed69248d25 galaxyp parents: 2 diff changeset	503 <!-- <test expect_num_outputs="2">
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	504 <section name="input">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	505 <param name="f" value="ThyroglobMRM000003.d.tar" />
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	506 <section name="spectral_lib_options">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	507 <param name="gen_spec_lib" value="True"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	508 <param name="predictor" value="True"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	509 </section>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	510 <section name="fasta_db_options">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	511 <param name="fasta" value="bsa.fasta"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	512 <param name="fasta_search" value="True"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	513 </section>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	514 </section>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	515 <output name="output_report" file="bruker-report.tsv">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	516 <assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	517 <has_text text="PG.Normalised"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	518 </assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	519 </output>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	520 <output name="output_report_lib" file="bruker-report-lib.tsv">
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	521 <assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	522 <has_text text="PrecursorMz"/>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	523 </assert_contents>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	524 </output>
65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	525 </test> -->
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	526 </tests>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	527 <help>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	528 <![CDATA[
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	529 DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing by Demichev, Ralser and Lilley labs.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	530
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	531 In 2018, DIA-NN opened a new chapter in proteomics, introducing a number of algorithms which enabled reliable, robust and quantitatively accurate large-scale experiments using high-throughput methods.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	532
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	533
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	534 DIA-NN is built on the following principles:
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	535
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	536 - Reliability achieved via stringent statistical control
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	537 - Robustness achieved via flexible modelling of the data and automatic parameter selection
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	538 - Reproducibility promoted by thorough recording of all analysis steps
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	539 - Ease of use: high degree of automation, an analysis can be set up in several mouse clicks, no bioinformatics expertise required
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	540 - Powerful tuning options to enable unconventional experiments
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	541 - Scalability and speed: up to 1000 mass spec runs processed per hour
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	542
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	543 Raw data formats
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	544
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	545 Formats supported: Sciex .wiff, Bruker .d, Thermo .raw, .mzML and .dia (format used by DIA-NN to store spectra). Conversion from any supported format to .dia is possible. When running on Linux (native builds, not Wine), only .d, .mzML, and .dia data are supported.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	546
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	547 For .wiff support, download and install ProteoWizard - choose the version (64-bit) that supports "vendor files"). Then copy all files with 'Clearcore' or 'Sciex' in their name (these will be .dll files) from the ProteoWizard folder to the DIA-NN installation folder (the one which contains diann.exe, DIA-NN.exe and a bunch of other files).
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	548
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	549 Reading Thermo .raw files requires Thermo MS File Reader to be installed. It is essential to use specifically the version by the link above (3.0 SP3).
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	550
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	551 .mzML files should be centroided and contain data as spectra (e.g. SWATH) and not chromatograms.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	552
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	553 Spectral library formats
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	554
2 65134626eb2b planemo upload for repository https://github.com/vdemichev/DiaNN commit 005bb8d9fa17c3f28b960d99b23947841e06d90a galaxyp parents: 1 diff changeset	555 DIA-NN supports comma-separated (.csv) or tab-separated (.tsv, .xls or .txt), .speclib (compact format used by DIA-NN), .sptxt (SpectraST, experimental [not in Galaxy]) and .msp (NIST, experimental [not in Galaxy]) library files. Important: the library must not contain non-fragmented precursor ions as 'fragments': each fragment ion must actually be produced by the peptide backbone fragmentation.
0 9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	556
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	557 Library-free search
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	558
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	559 DIA-NN has a very advanced library-free module, which is, for certain types of experiments, better than using a high quality project-specific spectral library. In general, the following makes library-free search perform better in comparison to spectral libraries (while the opposite favours spectral libraries):
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	560
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	561 - high peptide numbers detectable per run
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	562 - heterogeneous data (e.g. cancer tissue samples are quite heterogeneous, while replicate injections of the same sample are not)
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	563 - long chromatographic gradients as well as good separation of peptides in the ion mobility dimension
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	564 - large dataset (although processing a large dataset in library-free mode might take time)
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	565
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	566 Please note that in 99% of cases it is essential that MBR is enabled for a quantitative library-free analysis. It gets activated by default when using the DIA-NN GUI.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	567
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	568 For most experiments it does indeed make sense to try library-free search. For medium and large-scale experiments it might make sense to first try library-free analysis of a subset of the data, to see whether the performance is OK (on the whole dataset it will typically be a lot better, so no need to be too stringent here). Ourselves we also often perform a quick preliminary QC assessment of the experiment using some public library.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	569
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	570 It is often convenient to perform library-free analysis in two steps: by first creating an in silico-predicted spectral library from the sequence database, and then analysing with this library.
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	571
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	572 For more information, visit https://github.com/vdemichev/DiaNN
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	573 ]]>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	574 </help>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	575 <citations>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	576 <citation type="doi">10.1038/s41592-019-0638-x</citation>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	577 <citation type="doi">10.1038/s41467-021-25454-1</citation>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	578 <citation type="doi">10.1038/s41467-022-31492-0</citation>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	579 </citations>
9aa386e5f239 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	580 </tool>

Mercurial > repos > galaxyp > diann

annotate diann.xml @ 3:a8f461b7d193 draft default tip