maxquant: maxquant.xml annotate

annotate maxquant.xml @ 1:8bac3cc5c5de draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847

author	galaxyp
date	Sat, 20 Jul 2019 05:01:05 -0400
parents	d4b6c9eae635
children	175e062b6a17

rev	line source
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1 <tool id="maxquant" name="MaxQuant" version="@VERSION@">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	2 <macros>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	3 <import>macros.xml</import>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	4 </macros>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	5 <requirements>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	6 <requirement type="package" version="@VERSION@">maxquant</requirement>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	7 <requirement type="package" version="3.7">python</requirement>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	8 </requirements>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	9 <command detect_errors="exit_code"><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	10 #import re
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	11
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	12 python3 '$__tool_directory__/mqwrapper.py'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	13 --num_threads=\${GALAXY_SLOTS:-1}
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	14 --substitution_rx='@SUBSTITUTION_RX@'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	15 #if $input_opts.infile.select == "mzxml_files"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	16 --mzxml_files='$input_opts.infile.mzxml_files'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	17 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.mzxml_files])
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	18 #else
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	19 --raw_files='$input_opts.infile.raw_files'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	20 #set names = ','.join([re.sub('@SUBSTITUTION_RX@', '_', str($name.element_identifier)) for $name in $input_opts.infile.raw_files])
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	21 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	22 --infile_names='$names'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	23 --version='@VERSION@'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	24 --fasta_files='$input_opts.fasta_files'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	25 --identifier_parse_rule='$input_opts.identifier_parse_rule'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	26 --description_parse_rule='$input_opts.description_parse_rule'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	27
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	28 --exp_design='$search_opts.template'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	29 --missed_cleavages=$search_opts.missed_cleavages
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	30 --min_peptide_len=$search_opts.min_peptide_len
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	31 --max_peptide_mass=$search_opts.max_peptide_mass
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	32 --min_unique_pep=$search_opts.min_unique_pep
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	33 $search_opts.calc_peak_properties
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	34 $search_opts.match_between_runs
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	35 #if $search_opts.fixed_mods
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	36 --fixed_mods='$search_opts.fixed_mods'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	37 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	38 #if $search_opts.var_mods
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	39 --var_mods='$search_opts.var_mods'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	40 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	41 #if $search_opts.proteases
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	42 --proteases='$search_opts.proteases'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	43 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	44 #if $search_opts.silac.light_mods
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	45 --light_mods='$search_opts.silac.light_mods'
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	46 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	47 #if $search_opts.silac.medium_mods
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	48 --medium_mods='$search_opts.silac.medium_mods'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	49 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	50 #if $search_opts.silac.heavy_mods
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	51 --heavy_mods='$search_opts.silac.heavy_mods'
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	52 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	53 #if $search_opts.lfq.do_lfq == "--lfq_mode=1"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	54 $search_opts.lfq.do_lfq.lfq_mode
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	55 --lfq_min_ratio_count=$search_opts.lfq.do_lfq.lfq_min_ratio_count
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	56 --lfq_min_edges_per_node=$search_opts.lfq.do_lfq.lfq_min_edges_per_node
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	57 --lfq_avg_edges_per_node=$search_opts.lfq.do_lfq.lfq_avg_edges_per_node
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	58 $search_opts.lfq.do_lfq.lfq_skip_norm
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	59 $search_opts.lfq.do_lfq.separate_lfq
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	60 $search_opts.lfq.do_lfq.lfq_stabilize_large_ratios
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	61 $search_opts.lfq.do_lfq.lfq_require_msms
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	62 #if $search_opts.lfq.do_lfq.do_ibaq == "--ibaq"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	63 $search_opts.lfq.do_lfq.do_ibaq.ibaq
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	64 $search_opts.lfq.do_lfq.do_ibaq.ibaq_log_fit
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	65 #end if
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	66 $search_opts.lfq.do_lfq.advanced_site_intensities
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	67 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	68
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	69 $output_opts.write_mztab
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	70 --evidence='$evidence'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	71 --msms='$msms'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	72 --parameters='$parameters'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	73 --peptides='$peptides'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	74 --proteinGroups='$proteinGroups'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	75 --allPeptides='$allPeptides'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	76 --libraryMatch='$libraryMatch'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	77 --matchedFeatures='$matchedFeatures'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	78 --modificationSpecificPeptides='$modificationSpecificPeptides'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	79 --ms3Scans='$ms3Scans'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	80 --msmsScans='$msmsScans'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	81 --mzRange='$mzRange'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	82 --peptideSection='$peptideSection'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	83 --summary='$summary'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	84 --mzTab='$mzTab'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	85 --mqpar_out='$mqpar_out'
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	86
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	87 #if 'log' in $output_opts.output
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	88 > '$log'
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	89 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	90 #if 'output_all' in $output_opts.output
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	91 && tar -zcf '$output_all' ./combined/txt
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	92 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	93 ]]></command>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	94 <inputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	95 <section name="input_opts" title="Input Options" expanded="True">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	96 <conditional name="infile">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	97 <param name="select" type="select" label="choose the type of your input files">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	98 <option value="raw_files">Thermo.raw</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	99 <option value="mzxml_files">mzXML</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	100 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	101 <when value="raw_files">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	102 <param multiple="true" name="raw_files" type="data"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	103 format="thermo.raw" label="RAW Files"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	104 help="Specify one or more Thermo RAW files" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	105 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	106 <when value="mzxml_files">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	107 <param multiple="true" name="mzxml_files" type="data"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	108 format="mzxml" label="mzXML Files"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	109 help="Specify one or more mzXML files" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	110 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	111 </conditional>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	112 <param format="fasta" multiple="true" name="fasta_files"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	113 type="data" label="FASTA files"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	114 help="Specify one or more FASTA databases." />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	115 <param name="identifier_parse_rule" type="text"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	116 label="identifier parse rule" value="^>.\\|(.)\\|.*$">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	117 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	118 <valid initial="string.printable">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	119 <remove value="'"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	120 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	121 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	122 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	123 <param name="description_parse_rule" type="text"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	124 label="description parse rule" value="^>.\\|.\\|[^ ]+ (.) OS.$"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	125 help="Modify parse rules if needed">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	126 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	127 <valid initial="string.printable">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	128 <remove value="'"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	129 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	130 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	131 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	132 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	133
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	134 <section name="search_opts" title="Search Options" expanded="true">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	135 <param format="tabular" name="template" type="data" optional="true"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	136 label="Specify an experimental design template (if needed). For detailed
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	137 instructions see the help text." />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	138 <param type="integer" name="missed_cleavages"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	139 label="missed cleavages" value="1"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	140 <param type="integer" name="min_peptide_len"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	141 label="minimum peptide length" value="7"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	142 <param type="integer" name="max_peptide_mass"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	143 label="maximum peptide mass" value="4600"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	144 <param type="integer" name="min_unique_pep"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	145 label="minimum unique peptides" value="1" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	146 <param name="calc_peak_properties" type="boolean" checked="false"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	147 label="Calculate peak properties?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	148 truevalue="--calc_peak_properties" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	149 <param name="match_between_runs" type="boolean" checked="false"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	150 label="Match between runs?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	151 truevalue="--match_between_runs" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	152 <param name="fixed_mods" type="select" label="fixed modifications"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	153 multiple="true" help="select zero or more fixed modifications">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	154 <expand macro="modification"/>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	155 </param>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	156 <param name="var_mods" type="select" label="variable modifications"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	157 multiple="true" help="select zero or more variable modifications">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	158 <expand macro="modification"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	159 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	160 <param name="proteases" type="select" label="proteases"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	161 multiple="true" help="select zero or more proteases">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	162 <expand macro="proteases"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	163 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	164 <section title="label based quantitation" name="silac" expanded="false">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	165 <param name="light_mods" type="select" label="light labels"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	166 multiple="true" help="select zero or more light modifications">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	167 <expand macro="label"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	168 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	169 <param name="medium_mods" type="select" label="medium labels"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	170 multiple="true" help="select zero or more medium modifications">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	171 <expand macro="label"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	172 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	173 <param name="heavy_mods" type="select" label="heavy labels"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	174 multiple="true" help="select zero or more heavy modifications">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	175 <expand macro="label"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	176 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	177 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	178 <section title="label free quantification" name="lfq" expanded="false">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	179 <conditional name="do_lfq">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	180 <param name="lfq_mode" type="select" label="Perform LFQ?">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	181 <option value="">No</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	182 <option value="--lfq_mode=1">Yes</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	183 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	184 <when value="--lfq_mode=1">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	185 <param type="integer" name="lfq_min_ratio_count"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	186 label="LFQ minimum ratio count" value="2"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	187 <param type="integer" name="lfq_min_edges_per_node"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	188 label="LFQ minimum number of neighbours" value="3"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	189 <param type="integer" name="lfq_avg_edges_per_node"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	190 label="LFQ average number of neighbours" value="6"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	191 <param name="lfq_skip_norm" type="boolean" checked="false"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	192 label="Skip normalization?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	193 truevalue="--lfq_skip_norm" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	194 <param name="separate_lfq" type="boolean" checked="false"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	195 label="Separate LFQ in parameter Groups?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	196 truevalue="--separate_lfq" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	197 <param name="lfq_stabilize_large_ratios" type="boolean" checked="true"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	198 label="Stabilize large LFQ ratios?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	199 truevalue="--lfq_stabilize_large_ratios" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	200 <param name="lfq_require_msms" type="boolean" checked="true"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	201 label="Require MS/MS for LFQ comparisons?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	202 truevalue="--lfq_require_msms" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	203 <conditional name="do_ibaq">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	204 <param name="ibaq" type="select" label="iBAQ?">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	205 <option value="">No</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	206 <option value="--ibaq">Yes</option>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	207 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	208 <when value="--ibaq">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	209 <param name="ibaq_log_fit" type="boolean" checked="true"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	210 label="Logarithmic fit?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	211 truevalue="--ibaq_log_fit" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	212 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	213 <when value="">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	214 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	215 </conditional>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	216 <param name="advanced_site_intensities" type="boolean" checked="true"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	217 label="Advanced site intensities?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	218 truevalue="--advanced_site_intensities" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	219 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	220 <when value="">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	221 </when>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	222 </conditional>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	223 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	224 </section>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	225
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	226 <section title="Output Options" name="output_opts" expanded="true">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	227 <param name="write_mztab" type="boolean" checked="false"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	228 label="Write mztab file?"
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	229 truevalue="--write_mztab" falsevalue="" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	230 <param type="select" name="output" label="Select the desired outputs."
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	231 multiple="true" optional="false">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	232 <expand macro="output_option" name="proteinGroups" label="Protein Groups"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	233 <expand macro="output_option" name="mqpar_out" label="mqpar.xml"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	234 <expand macro="output_option" name="peptides" label="Peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	235 <expand macro="output_option" name="evidence" label="Evidence"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	236 <expand macro="output_option" name="parameters" label="Tabular Paramters"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	237 <expand macro="output_option" name="msms" label="MSMS"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	238 <expand macro="output_option" name="mzTab" label="mzTab"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	239 <expand macro="output_option" name="allPeptides" label="all peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	240 <expand macro="output_option" name="libraryMatch" label="library match"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	241 <expand macro="output_option" name="matchedFeatures" label="matched features"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	242 <expand macro="output_option" name="modificationSpecificPeptides" label="modification specific peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	243 <expand macro="output_option" name="ms3Scans" label="ms3 scans"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	244 <expand macro="output_option" name="msmsScans" label="msms scans"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	245 <expand macro="output_option" name="mzRange" label="mz range"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	246 <expand macro="output_option" name="peptideSection" label="peptide section"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	247 <expand macro="output_option" name="summary" label="summary"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	248 <expand macro="output_option" name="output_all" label="complete 'combined/txt/' directory (compressed)"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	249 <expand macro="output_option" name="log" label="MaxQuant log"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	250 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	251 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	252 </inputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	253
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	254 <outputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	255 <expand macro="output" name="proteinGroups" label="MaxQuant Protein Groups"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	256 <expand macro="output" name="mqpar_out" label="mqpar.xml" format="xml"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	257 <expand macro="output" name="peptides" label="MaxQuant Peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	258 <expand macro="output" name="evidence" label="MaxQuant Evidence"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	259 <expand macro="output" name="parameters" label="MaxQuant Tabular Parameters"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	260 <expand macro="output" name="msms" label="MaxQuant MSMS"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	261 <expand macro="output" name="mzTab" label="mzTab"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	262 <expand macro="output" name="allPeptides" label="all peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	263 <expand macro="output" name="libraryMatch" label="library match"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	264 <expand macro="output" name="matchedFeatures" label="matched features"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	265 <expand macro="output" name="modificationSpecificPeptides" label="modification specific peptides"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	266 <expand macro="output" name="ms3Scans" label="ms3 scans"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	267 <expand macro="output" name="msmsScans" label="msms Scans"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	268 <expand macro="output" name="mzRange" label="mz range"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	269 <expand macro="output" name="peptideSection" label="peptide section"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	270 <expand macro="output" name="summary" label="MaxQuant summary"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	271 <expand macro="output" format="tar" name="output_all" label="'combined/txt/' directory"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	272 <expand macro="output" name="log" format="txt" label="log"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	273 </outputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	274
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	275 <tests>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	276 <test>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	277 <param name="select" value="mzxml_files" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	278 <param name="mzxml_files" value="BSA_min_23.mzXML" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	279 <param name="fasta_files" value="bsa.fasta" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	280 <param name="identifier_parse_rule" value=">([^\s]*)" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	281 <param name="description_parse_rule" value=">(.*)" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	282 <param name="min_unique_pep" value="0" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	283 <param name="fixed_mods" value="Carbamidomethyl (C)" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	284 <param name="var_mods" value="Oxidation (M)" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	285 <param name="proteases" value="Trypsin/P" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	286 <param name="write_mztab" value="true" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	287 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	288 <output name="evidence" file="single/combined/txt/evidence.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	289 <output name="msms" file="single/combined/txt/msms.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	290 <output name="mzTab" file="single/combined/txt/mzTab.mzTab" lines_diff="4"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	291 <output name="allPeptides" file="single/combined/txt/allPeptides.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	292 <output name="msmsScans" file="single/combined/txt/msmsScans.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	293 <output name="mzRange" file="single/combined/txt/mzRange.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	294 <output name="parameters" file="single/combined/txt/parameters.txt" lines_diff="10"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	295 <output name="peptides" file="single/combined/txt/peptides.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	296 <output name="peptideSection" file="single/combined/txt/peptideSection.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	297 <output name="proteinGroups" file="single/combined/txt/proteinGroups.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	298 <output name="summary" file="single/combined/txt/summary.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	299 <output name="modificationSpecificPeptides" file="single/combined/txt/modificationSpecificPeptides.txt" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	300 </test>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	301 </tests>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	302
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	303 <help><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	304 MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	305
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	306 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a very reduced set of search parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too. If possible, this tool should be preferred.
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	307
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	308 Input files
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	309
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	310 - Thermo raw file or mzXML file
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	311 - The datatype has to be 'thermo.raw' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	312 - Optional files:
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	313 - Tabular file with experimental design template:
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	314 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Fraction are abitrary strings, Experiment is an integer, PTM is either True or False.
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	315
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	316 ::
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	317
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	318 Name Fraction Experiment PTM
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	319 File1 1 E1 False
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	320 File2 2 E1 False
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	321 File3 3 E1 False
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	322 ...
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	323 ...
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	324
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	325 Parameter Options
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	326
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	327 - Quantification options
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	328 - label based:
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	329 - for two channels: choose options from light and heavy sections, for three channels choose options from light, medium and heavy sections
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	330 - label-free
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	331
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	332 Output files
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	333
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	334 Different output file options are available, most of them are part of the MaxQuant txt directory.
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	335 ]]></help>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	336 <citations>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	337 <citation type="bibtex">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	338 @article{cox2008maxquant,
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	339 title={MaxQuant enables high peptide identification rates, individualized
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	340 ppb-range mass accuracies and proteome-wide protein quantification},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	341 author={Cox, J{\"u}rgen and Mann, Matthias},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	342 journal={Nature biotechnology},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	343 volume={26},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	344 number={12},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	345 pages={1367},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	346 year={2008},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	347 publisher={Nature Publishing Group}
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	348 }
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	349 </citation>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	350 <citation type="bibtex">
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	351 @article{tyanova2016maxquant,
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	352 title={The MaxQuant computational platform for mass
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	353 spectrometry-based shotgun proteomics},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	354 author={Tyanova, Stefka and Temu, Tikira and Cox, J{\"u}rgen},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	355 journal={Nature protocols},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	356 volume={11},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	357 number={12},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	358 pages={2301},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	359 year={2016},
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	360 publisher={Nature Publishing Group}
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	361 }
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	362 </citation>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	363 </citations>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	364 </tool>

Mercurial > repos > galaxyp > maxquant

annotate maxquant.xml @ 1:8bac3cc5c5de draft