diann: diann.xml annotate

annotate diann.xml @ 1:ae4dc0c041f9 draft

planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71

author	galaxyp
date	Mon, 02 Oct 2023 14:15:42 +0000
parents	9fa3dbf06f17
children	bf0728e000cd

rev	line source
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
9fa3dbf06f17 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>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	3 <macros>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	4 <token name="@TOOL_VERSION@">1.8.1</token>
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	5 <token name="@VERSION_SUFFIX@">1</token>
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	6 </macros>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	7 <requirements>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	8 <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	9 </requirements>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	11 mkdir ./input_data &&
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	12 mkdir ./tmp &&
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	13
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	14 ## generate string like "--f file1 --f file2 ..." for each input in $input.f, which are comma separated
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	15 #set infiles_str = ''
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	16 #for $infile in $input.f
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	17 ## if brukertdf.d.tar, extract to ./input_data and append "./input_data/" to infiles_str
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	18 #if $infile.is_of_type("brukertdf.d.tar"):
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	19 tar -xf '$infile' -C ./input_data &&
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	20 #set $infiles_str += '--f ./input_data/' + str($infile.element_identifier[:-4]) + ' '
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	21 #else
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	22 ln -s '$infile' './input_data/$infile.element_identifier' &&
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	23 #set $infiles_str += '--f ./input_data/' + str($infile.element_identifier)
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	24 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	25 #end for
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	26
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	27 #set $fasta_file_str = ''
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	28 #for $fasta_file in $input.fasta_db_options.fasta
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	29 #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	30 #end for
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	31
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	32 diann
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	33 #if $input.f != 'None'
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	34 '$infiles_str'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	35 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	36 --dir ./
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	37 #if $input.spectral_lib_options.lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	38 --lib '$input.spectral_lib_options.lib'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	39 #else
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	40 --lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	41 #end if
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	42 #if $input.f != 'None'
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	43 --out ./report.tsv
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	44 #end if
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	45 #if $input.spectral_lib_options.gen_spec_lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	46 --out-lib ./report-lib.tsv
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	47 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	48 --threads \${GALAXY_SLOTS:-1}
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	49 --temp ./tmp
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	50
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	51 ## Spectral library options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	52 $input.spectral_lib_options.gen_spec_lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	53 #if $input.spectral_lib_options.library_headers
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	54 --library-headers '$input.spectral_lib_options.library_headers'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	55 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	56 $input.spectral_lib_options.no_lib_filter
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	57 #if $input.spectral_lib_options.learn_lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	58 --learn-lib '$input.spectral_lib_options.learn_lib'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	59 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	60 $input.spectral_lib_options.out_measured_rt
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	61 $input.spectral_lib_options.predictor
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	62 $input.spectral_lib_options.reannotate
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	63 #if $input.spectral_lib_options.ref
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	64 --ref '$input.spectral_lib_options.ref'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	65 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	66
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	67 ## FASTA database options
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	68 #if $fasta_file_str != 'None'
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	69 '$fasta_file_str'
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	70 #end if
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	71 #if $input.fasta_db_options.fasta_filter
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	72 --fasta-filter '$input.fasta_db_options.fasta_filter'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	73 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	74 $input.fasta_db_options.fasta_search
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	75
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	76 ## Algorithm options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	77 $algo_options.no_calibration
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	78 #if $algo_options.mass_acc
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	79 --mass-acc '$algo_options.mass_acc'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	80 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	81 #if $algo_options.mass_acc_cal
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	82 --mass-acc-cal '$algo_options.mass_acc_cal'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	83 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	84 #if $algo_options.mass_acc_ms1
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	85 --mass-acc-ms1 '$algo_options.mass_acc_ms1'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	86 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	87 $algo_options.quick_mass_acc
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	88 $algo_options.reanalyse
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	89 $algo_options.mbr_fix_settings
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	90 $algo_options.relaxed_prot_inf
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	91 $algo_options.prot_inf
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	92 $algo_options.nn_classifier
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	93 $algo_options.quant_strategy
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	94 $algo_options.cross_run_norm
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	95 $algo_options.lib_gen_strategy
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	96
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	97 ## Ion mobility options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	98 ## ToDo: no_im_window as condition?
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	99 $im_window_options.no_im_window
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	100 #if $im_window_options.window
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	101 --window '$im_window_options.window'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	102 --im-window '$im_window_options.im_window'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	103 --im-window-factor '$im_window_options.im_window_factor'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	104 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	105
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	106 ## Precursor options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	107 --cut '$precursor_options.cleavage_spec.cut'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	108 --missed-cleavages '$precursor_options.missed_cleavages'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	109 $precursor_options.met_excision
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	110 --min-pep-len '$precursor_options.min_pep_len'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	111 --max-pep-len '$precursor_options.max_pep_len'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	112 --min-pr-mz '$precursor_options.min_pr_mz'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	113 --max-pr-mz '$precursor_options.max_pr_mz'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	114 --min-pr-charge '$precursor_options.min_pr_charge'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	115 --max-pr-charge '$precursor_options.max_pr_charge'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	116 --min-fr-mz '$precursor_options.min_fr_mz'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	117 --max-fr-mz '$precursor_options.max_fr_mz'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	118 $precursor_options.nn_single_seq
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	119 #if $precursor_options.int_removal
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	120 --int-removal '$precursor_options.int_removal'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	121 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	122
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	123 ## Fragment options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	124 $mass_frag_options.no_fr_selection
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	125 #if $mass_frag_options.quant_fr
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	126 --quant-fr '$mass_frag_options.quant_fr'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	127 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	128 $mass_frag_options.restrict_fr
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	129 #if $mass_frag_options.sptxt_acc
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	130 --sptxt-acc '$mass_frag_options.sptxt_acc'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	131 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	132 #if $mass_frag_options.target_fr
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	133 --target-fr '$mass_frag_options.target_fr'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	134 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	135
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	136 ## Channel options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	137 ## ToDo: no_decoy_channel as condition?
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	138 #if $channel_options.channels
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	139 --channels '$channel_options.channels'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	140 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	141 #if $channel_options.decoy_channel
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	142 --decoy-channel '$channel_options.decoy_channel'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	143 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	144 $channel_options.no_decoy_channel
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	145
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	146 ## Modification options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	147 #if $mod_options.fixed_mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	148 --fixed-mod '$mod_options.fixed_mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	149 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	150 #if $mod_options.var_mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	151 --var-mod '$mod_options.var_mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	152 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	153 #if $mod_options.var_mods
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	154 --var-mods '$mod_options.var_mods'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	155 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	156 #if $mod_options.mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	157 --mod '$mod_options.mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	158 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	159 #if $mod_options.monitor_mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	160 --monitor-mod '$mod_options.monitor_mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	161 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	162 #if $mod_options.no_cut_after_mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	163 --no-cut-after-mod '$mod_options.no_cut_after_mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	164 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	165 $mod_options.original_mods
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	166 $mod_options.clear_mods
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	167 #if $mod_options.lib_fixed_mod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	168 --lib-fixed-mod '$mod_options.lib_fixed_mod'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	169 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	170 $mod_options.mod_only
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	171 $mod_options.strip_unknown_mods
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	172 $mod_options.unimod4
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	173 $mod_options.unimod35
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	174
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	175 ## Quantification options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	176 $quantification_options.peak_translation
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	177 $quantification_options.no_maxlfq
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	178
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	179 ## Other options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	180 #if $other_options.min_peak
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	181 --min-peak '$other_options.min_peak'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	182 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	183 $other_options.no_rt_window
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	184 $other_options.no_stratification
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	185 $other_options.no_swissprot
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	186 $other_options.dl_no_im
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	187 $other_options.dl_no_rt
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	188 $other_options.duplicate_proteins
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	189 $other_options.exact_fdr
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	190 $other_options.force_swissprot
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	191 $other_options.full_unimod
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	192 $other_options.gen_fr_restriction
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	193 $other_options.global_mass_cal
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	194 $other_options.il_eq
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	195 $other_options.individual_mass_acc
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	196 $other_options.individual_reports
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	197 $other_options.individual_windows
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	198 $other_options.no_isotopes
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	199 $other_options.regular_swath
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	200 $other_options.scanning_swath
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	201 $other_options.semi
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	202 $other_options.species_genes
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	203 $other_options.tims_skip_errors
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	204
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	205 ## Output options
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	206 $output_options.no_main_report
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	207 $output_options.no_stats
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	208 $output_options.compact_report
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	209 $output_options.matrices
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	210 #if $output_options.matrix_ch_qvalue
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	211 --matrix-ch-qvalue '$output_options.matrix_ch_qvalue'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	212 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	213 --qvalue $output_options.qvalue
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	214 #if $output_options.matrix_tr_qvalue
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	215 --matrix-tr-qvalue '$output_options.matrix_tr_qvalue'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	216 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	217 $output_options.matrix_spec_q
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	218 $output_options.report_lib_info
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	219 #if $output_options.vis
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	220 --vis '$output_options.vis'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	221 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	222 --verbose '$output_options.verbose'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	223
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	224 #if len($input.f) > 0
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	225 && cp ./report.tsv '$output_report'
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	226 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	227
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	228 #if $input.spectral_lib_options.gen_spec_lib
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	229 && cp ./report-lib.tsv '$output_report_lib'
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	230 && cp ./report-lib.tsv.speclib '$output_report_speclib'
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	231 && cp ./report-lib.predicted.speclib '$output_report_pred_speclib'
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	232 #end if
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	233 ]]></command>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	234 <inputs>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	235 <!-- not used: cfg, convert, dir, ext, no_quant_files, out, out_lib, out_lib_copy, prefix, temp, threads, use-quant -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	236 <section name="input" expanded="true" title="Input files">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	237 <param name="f" type="data" format="mzml,dia,wiff,thermo.raw,brukertdf.d.tar" multiple="true" optional="true" label="Input file" help="Specify a run to be analysed"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	238 <!-- ToDo lib: The use of multiple lib commands (experimental) allows to load multiple libraries in .tsv format -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	239 <section name="spectral_lib_options" title="Spectral library">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	240 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	241 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	242 <param name="lib" type="data" format="csv,tsv,xls,txt,binary,speclib,sptxt,msp" optional="true" label="Spectral library" help="Specify a spectral library"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	243 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	244 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	245 <param name="learn_lib" type="data" format="tsv" optional="true" label="Training library" help="Specifies a 'training library' for the legacy predictor"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	246 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	247 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	248 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	249 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	250 <section name="fasta_db_options" title="FASTA database">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	251 <!-- ToDo fasta: use multiple fasta commands to specify multiple databases -->
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	252 <param name="fasta" type="data" format="fasta" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	253 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	254 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	255 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	256 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	257 <section name="algo_options" title="Algorithm">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	258 <param name="no_calibration" type="boolean" truevalue="--no-calibration" falsevalue="" checked="false" label="Disable mass calibration" help="Disables mass calibration"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	259 <param name="mass_acc" type="float" min="0" optional="true" label="MS2 mass accuracy" help="Sets the MS2 mass accuracy to N ppm"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	260 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	261 <param name="mass_acc_ms1" type="float" min="0" optional="true" label="MS1 mass accuracy" help="Sets the MS1 mass accuracy to N ppm"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	262 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	263 <!-- ToDo mbr_fix_settings: what does 'Unrelated runs' mean? -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	264 <param name="reanalyse" type="boolean" truevalue="--reanalyse" falsevalue="" checked="false" label="Enable MBR" help="Enables MBR"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	265 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	266 <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."/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	267 <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">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	268 <option value="--pg-level 0">Isoform IDs</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	269 <option value="--pg-level 1">Protein names (from FASTA)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	270 <option value="--pg-level 2">Genes (species-specific)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	271 <option value="" selected="True">Genes</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	272 <option value="--no-prot-inf">Off</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	273 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	274 <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">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	275 <option value="" selected="True">Single-pass mode</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	276 <option value="--double-search">Double-pass mode</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	277 <option value="--no-nn">off</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	278 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	279 <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.">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	280 <option value="">Any LC (high accuracy)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	281 <option value="--no-ifs-removal">Any LC (high precision)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	282 <option value="--peak-center">Robust LC (high accuracy)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	283 <option value="--peak-center --no-ifs-removal" selected="True">Robust LC (high precision)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	284 <option value="--peak-height">Peak-height</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	285 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	286 <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">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	287 <option value="--global-norm">Global</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	288 <option value="" selected="True">RT-dependent</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	289 <option value="--sig-norm">RT and signal-dep. (experimental)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	290 <option value="--no-norm">Off</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	291 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	292 <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">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	293 <option value="--id-profiling">IDs profiling</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	294 <option value="--rt-profiling">IDs, RT and IM profiling</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	295 <option value="--smart-profiling" selected="true">Smart profiling</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	296 <option value="">Full profiling</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	297 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	298 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	299 <section name="im_window_options" title="Ion mobility window">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	300 <param name="no_im_window" type="boolean" truevalue="--no-im-window" falsevalue="" checked="false" label="Disable IM-windowed search" help="Disables IM-windowed search"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	301 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	302 <param name="im_window" type="integer" min="0" optional="true" label="IM extraction window" help="Fixes IM extraction window to the specific value"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	303 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	304 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	305 <section name="precursor_options" title="Precursor ion generation">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	306 <conditional name="cleavage_spec">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	307 <param name="cut_type" type="select" label="Cleavage specificity">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	308 <option value="predefined">Predefined cleavage pattern</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	309 <option value="own">Define your own cleavage pattern</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	310 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	311 <when value="predefined">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	312 <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">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	313 <option value="K,R" selected="true">Trypsin/P</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	314 <option value="K,R,!P">Trypsin (excluding cuts at P)</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	315 <option value="K*">Lys-C</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	316 <option value="F,Y,W,M,L,!P">Chymotrypsin</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	317 <option value="*D">AspN</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	318 <option value="E*">GluC</option>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	319 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	320 </when>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	321 <when value="own">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	322 <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.">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	323 </param>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	324 </when>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	325 </conditional>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	326 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	327 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	328 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	329 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	330 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	331 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	332 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	333 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	334 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	335 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	336 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	337 <param name="int_removal" type="integer" min="0" optional="true" label="Interference removal" help="Specify 0 to disable the removal of interfering precursors"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	338 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	339 <section name="mod_options" title="Modifications">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	340 <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']"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	341 <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." />
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	342 <param name="var_mods" type="integer" min="0" optional="true" label="Maximum number of variable modifications" help="Sets the maximum number of variable modifications"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	343 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	344 <!-- ToDo monitor_mod: This modification must have been declared as variable using var-mod -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	345 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	346 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	347 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	348 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	349 <param name="lib_fixed_mod" type="text" label="In silico modification" help="Applies a modification, previously declared using --fixed-mod, to a spectral library"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	350 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	351 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	352 <param name="unimod4" type="boolean" truevalue="--unimod4" falsevalue="" checked="true" label="Considers C carbamidomethylation" help=""/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	353 <param name="unimod35" type="boolean" truevalue="--unimod35" falsevalue="" checked="false" label="Considers Ox(M) methionine oxidation" help=""/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	354 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	355 <section name="mass_frag_options" title="Mass calibration and Fragmentation">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	356 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	357 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	358 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	359 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	360 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	361 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	362 <section name="channel_options" title="Channel">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	363 <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."/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	364 <param name="decoy_channel" type="text" optional="true" label="Decoy channel" help="Specifies the decoy channel masses (same syntax as for --channels)"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	365 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	366 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	367 <section name="quantification_options" title="Quantification">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	368 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	369 <param name="no_maxlfq" type="boolean" truevalue="--no-maxlfq" falsevalue="" checked="false" label="Disable MaxLFQ for protein quantification" help="Disables MaxLFQ for protein quantification"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	370 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	371 <section name="other_options" title="Other">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	372 <param name="min_peak" type="float" min="0.01" optional="true" label="Minimum peak height" help="Sets the minimum peak height to consider"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	373 <param name="no_rt_window" type="boolean" truevalue="--no-rt-window" falsevalue="" checked="false" label="Disable RT-windowed search" help="Disables RT-windowed search"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	374 <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."/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	375 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	376 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	377 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	378 <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)"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	379 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	380 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	381 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	382 <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)"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	383 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	384 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	385 <!-- ToDo individual_mass_acc: what does automatic mean? -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	386 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	387 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	388 <!-- ToDo individual_windows: what does automatic mean? -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	389 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	390 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	391 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	392 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	393 <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)"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	394 <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."/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	395 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	396 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	397 <section name="output_options" expanded="true" title="Output">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	398 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	399 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	400 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	401 <param name="matrices" type="boolean" truevalue="--matrices" falsevalue="" checked="true" label="Output quantities matrices" help="Outputs quantities matrices"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	402 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	403 <param name="qvalue" type="float" min="0" value="0.01" label="q-value" help="Sets the q-value used to filter the output matrices"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	404 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	405 <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."/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	406 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	407 <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"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	408 <param name="verbose" type="integer" min="0" max="4" value="1" label="Verbose level" help="Sets the level of detail of the log"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	409 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	410 </inputs>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	411 <outputs>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	412 <data format="tabular" name="output_report" label="${tool.name} on ${on_string}: report.tsv">
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	413 <filter>input['f'] != None</filter>
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	414 </data>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	415 <data format="tabular" name="output_report_lib" label="${tool.name} on ${on_string}: report-lib.tsv">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	416 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	417 </data>
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	418 <data format="data" name="output_report_speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	419 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	420 </data>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	421 <data format="data" name="output_report_pred_speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	422 <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	423 </data>
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	424 </outputs>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	425 <tests>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	426 <!-- test for default run -->
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	427 <test expect_num_outputs="4">
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	428 <section name="input">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	429 <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	430 <section name="spectral_lib_options">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	431 <param name="gen_spec_lib" value="True"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	432 <param name="predictor" value="True"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	433 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	434 <section name="fasta_db_options">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	435 <param name="fasta" value="bsa.fasta"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	436 <param name="fasta_search" value="True"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	437 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	438 </section>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	439 <output name="output_report" file="report.tsv">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	440 <assert_contents>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	441 <has_text text="PG.Normalised"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	442 </assert_contents>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	443 </output>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	444 <output name="output_report_lib" file="report-lib.tsv">
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	445 <assert_contents>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	446 <has_text text="PrecursorMz"/>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	447 </assert_contents>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	448 </output>
1 ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	449 <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	450 <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	451 </test>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	452 <!-- test for multiple fastas -->
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	453 <test expect_num_outputs="1">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	454 <section name="input">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	455 <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	456 <section name="fasta_db_options">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	457 <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	458 <param name="fasta_search" value="True"/>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	459 </section>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	460 </section>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	461 <output name="output_report" file="report.tsv">
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	462 <assert_contents>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	463 <has_text text="PG.Normalised"/>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	464 </assert_contents>
ae4dc0c041f9 planemo upload for repository https://github.com/vdemichev/DiaNN commit c2518a175b19e8f6b81c64d2699677e82bce9c71 galaxyp parents: 0 diff changeset	465 </output>
0 9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	466 </test>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	467 <!-- test for Bruker data -->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	468 <!-- <test expect_num_outputs="2">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	469 <!-- <section name="input">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	470 <!-- <param name="f" value="ThyroglobMRM000003.d.tar" />-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	471 <!-- <section name="spectral_lib_options">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	472 <!-- <param name="gen_spec_lib" value="True"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	473 <!-- <param name="predictor" value="True"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	474 <!-- </section>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	475 <!-- <section name="fasta_db_options">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	476 <!-- <param name="fasta" value="bsa.fasta"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	477 <!-- <param name="fasta_search" value="True"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	478 <!-- </section>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	479 <!-- </section>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	480 <!-- <output name="output_report" file="bruker-report.tsv">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	481 <!-- <assert_contents>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	482 <!-- <has_text text="PG.Normalised"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	483 <!-- </assert_contents>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	484 <!-- </output>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	485 <!-- <output name="output_report_lib" file="bruker-report-lib.tsv">-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	486 <!-- <assert_contents>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	487 <!-- <has_text text="PrecursorMz"/>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	488 <!-- </assert_contents>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	489 <!-- </output>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	490 <!-- </test>-->
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	491 </tests>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	492 <help>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	493 <![CDATA[
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	494 DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing by Demichev, Ralser and Lilley labs.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	495
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	496 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	497
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	498
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	499 DIA-NN is built on the following principles:
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	500
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	501 - Reliability achieved via stringent statistical control
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	502 - Robustness achieved via flexible modelling of the data and automatic parameter selection
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	503 - Reproducibility promoted by thorough recording of all analysis steps
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	504 - Ease of use: high degree of automation, an analysis can be set up in several mouse clicks, no bioinformatics expertise required
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	505 - Powerful tuning options to enable unconventional experiments
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	506 - Scalability and speed: up to 1000 mass spec runs processed per hour
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	507
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	508 Raw data formats
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	509
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	510 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	511
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	512 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).
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	513
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	514 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).
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	515
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	516 .mzML files should be centroided and contain data as spectra (e.g. SWATH) and not chromatograms.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	517
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	518 Spectral library formats
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	519
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	520 DIA-NN supports comma-separated (.csv) or tab-separated (.tsv, .xls or .txt), .speclib (compact format used by DIA-NN), .sptxt (SpectraST, experimental) and .msp (NIST, experimental) 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	521
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	522 Library-free search
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	523
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	524 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):
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	525
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	526 - high peptide numbers detectable per run
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	527 - heterogeneous data (e.g. cancer tissue samples are quite heterogeneous, while replicate injections of the same sample are not)
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	528 - long chromatographic gradients as well as good separation of peptides in the ion mobility dimension
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	529 - large dataset (although processing a large dataset in library-free mode might take time)
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	530
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	531 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	532
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	533 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	534
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	535 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.
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	536
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	537 For more information, visit https://github.com/vdemichev/DiaNN
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	538 ]]>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	539 </help>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	540 <citations>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	541 <citation type="doi">10.1038/s41592-019-0638-x</citation>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	542 <citation type="doi">10.1038/s41467-021-25454-1</citation>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	543 <citation type="doi">10.1038/s41467-022-31492-0</citation>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	544 </citations>
9fa3dbf06f17 planemo upload for repository https://github.com/vdemichev/DiaNN commit 21426abf6bfe1d92f0598d35406f3bc315898628 galaxyp parents: diff changeset	545 </tool>

Mercurial > repos > galaxyp > diann

annotate diann.xml @ 1:ae4dc0c041f9 draft