maxquant: maxquant.xml annotate

annotate maxquant.xml @ 14:e42225f8a659 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d"

author	galaxyp
date	Thu, 08 Jul 2021 22:45:35 +0000
parents	181bd6a5f6ce
children	97a7f34fcb6a

rev	line source
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	1 <tool id="maxquant" name="MaxQuant" version="@VERSION@+galaxy@VERSION_SUFFIX@">
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	2 <macros>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	3 <xml name="output" token_format="tabular" token_label="default description" token_name="default">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	4 <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	5 <filter>'@NAME@' in output_opts['output']</filter>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	6 </data>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	7 </xml>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	8 <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	9 <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	10 <filter>'@NAME@' in output_opts['output']</filter>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	11 </data>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	12 </xml>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	13 <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	14 </macros>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	15 <expand macro="requirements"/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	16 <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	17 #import re
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	18 maxquant -c mqpar.xml 2>/dev/null ## MQ writes success of creation to stderr
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	19
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	20 ## Workaround for wrong MQ version in MaxQuantCmd.exe created mqpar.xml (1.6.5.0 instead of 1.6.17.0)
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	21 ## Should be removed as soon as MQ is updated with a fixed version
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	22 &&
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	23 sed -i -E 's:(maxQuantVersion>)1.6.5.0(<):\1'1.6.17.0'\2:' mqpar.xml
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	24 ## ==============================================================================================
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	25
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	26 #if 'config' in $output_opts.output:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	27 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	28 cp '$mq_conf' '$config'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	29 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	30 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	31 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	32 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	33 #for $target, $link in zip($infiles, $names_with_ext)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	34 &&
14 e42225f8a659 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d" galaxyp parents: 13 diff changeset	35 #if str($input_opts.ftype) == '.thermo.raw':
e42225f8a659 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d" galaxyp parents: 13 diff changeset	36 cp '$target' '$link'
e42225f8a659 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d" galaxyp parents: 13 diff changeset	37 #else:
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	38 ln -s '$target' '$link'
14 e42225f8a659 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d" galaxyp parents: 13 diff changeset	39 #end if
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	40 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	41 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	42 python3 '$__tool_directory__/create_mqpar.py'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	43 #if $search_opts.template
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	44 --exp_design='$search_opts.template'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	45 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	46 --version=@VERSION@
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	47 --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	48 --substitution_rx='@SUBSTITUTION_RX@'
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	49 --yaml='$mq_conf'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	50 mqpar.xml
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	51
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	52 #if $output_opts.dry_run:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	53 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	54 mkdir -p combined/txt
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	55 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	56 mv mqpar.xml combined/txt/mqpar.xml
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	57 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	58 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	59 maxquant mqpar.xml
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	60 #if 'log' in $output_opts.output:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	61 > '$log'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	62 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	63 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	64 mv mqpar.xml combined/txt/mqpar.xml
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	65 #if 'output_all' in $output_opts.output:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	66 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	67 tar -zcf '$output_all' ./combined/txt
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	68 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	69
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	70 #if $qc.do_it:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	71 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	72 Rscript '$qr' '$qr_yaml'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	73 #if 'log' in $output_opts.output:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	74 >> '$log' 2>&1
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	75 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	76 &&
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	77 cp './combined/txt/report_v@VERSION_PTXQC@_combined.pdf' '$ptxqc_report'
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	78 #end if
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	79 #end if
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	80 ]]></command>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	81
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	82 <configfiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	83 <configfile name="mq_conf">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	84 #import re
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	85 fastaFiles: [${input_opts.fasta_files}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	86 parseRules:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	87 identifierParseRule: '${input_opts.identifier_parse_rule}'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	88 descriptionParseRule: '${input_opts.description_parse_rule}'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	89 minUniquePeptides: ${search_opts.min_unique_pep}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	90 minPepLen: ${search_opts.min_peptide_len}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	91 maxPeptideMass: ${search_opts.max_peptide_mass}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	92 calcPeakProperties: ${search_opts.calc_peak_properties}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	93 #set writeMzTab = "mzTab" in $output_opts.output
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	94 writeMzTab: $writeMzTab
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	95 #if $protein_quant.lfq_opts.do_ibaq.ibaq == 'True':
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	96 ibaq: ${protein_quant.lfq_opts.do_ibaq.ibaq}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	97 ibaqLogFit: ${protein_quant.lfq_opts.do_ibaq.ibaqLogFit}
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	98 #end if
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	99 separateLfq: ${protein_quant.lfq_opts.separateLfq}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	100 lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	101 lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	102 advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	103 matchBetweenRuns: ${search_opts.mbr.match_between_runs}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	104 #if $search_opts.mbr.match_between_runs == 'True':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	105 matchingTimeWindow: ${search_opts.mbr.matching_time_window}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	106 matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	107 alignmentTimeWindow: ${search_opts.mbr.alignment_time_window}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	108 alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	109 matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	110 #end if
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	111 includeContaminants: ${search_opts.incl_contaminants}
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	112 minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	113 maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	114 decoyMode: ${search_opts.decoy_mode}
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	115 peptideFdr: ${search_opts.psm_fdr}
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	116 proteinFdr: ${search_opts.protein_fdr}
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	117 quantMode: ${protein_quant.peptides_for_quantification}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	118 restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	119 #if $protein_quant.only_unmod_prot.unmod_prot == 'True':
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	120 #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	121 restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	122 #else:
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	123 restrictMods: []
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	124 #end if
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	125 useCounterparts: $protein_quant.only_unmod_prot.discard_unmod_cpart_peptides
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	126 #end if
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	127 paramGroups:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	128 #for $pg in $paramGroups:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	129 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	130 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	131 - files: $names_with_ext
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	132 maxMissedCleavages: ${pg.maxMissedCleavages}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	133 #if $pg.fixedModifications:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	134 fixedModifications: [${pg.fixedModifications}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	135 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	136 fixedModifications: []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	137 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	138 #if $pg.variableModifications:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	139 variableModifications: [${pg.variableModifications}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	140 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	141 variableModifications: []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	142 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	143 #if $pg.enzymes:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	144 enzymes: [${pg.enzymes}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	145 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	146 enzymes: []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	147 #end if
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	148 enzymeMode: ${pg.digestion_mode}
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	149 #if $pg.quant_method.select_quant_method == 'silac':
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	150 labelMods:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	151 #if $pg.quant_method.light_labels:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	152 - [${pg.quant_method.light_labels}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	153 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	154 - []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	155 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	156 #if $pg.quant_method.medium_labels:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	157 - [${pg.quant_method.medium_labels}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	158 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	159 - []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	160 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	161 #if $pg.quant_method.heavy_labels:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	162 - [${pg.quant_method.heavy_labels}]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	163 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	164 - []
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	165 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	166 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	167 #if $pg.quant_method.select_quant_method == 'lfq':
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	168 lfqMode: 1
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	169 lfqNormType: ${pg.quant_method.lfqNormType}
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	170 lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	171 lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	172 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	173 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	174 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	175 lcmsRunType: 'Reporter ion MS2'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	176 reporterMassTolerance: 0.003
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	177 #if $pg.quant_method.filter_by_pif.filter_pif == 'True':
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	178 reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif}
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	179 #else:
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	180 reporterPif: 0
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	181 #end if
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	182 reporterFraction: 0
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	183 reporterBasePeakRatio: 0
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	184 filterPif: ${pg.quant_method.filter_by_pif.filter_pif}
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	185 isobaricLabels:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	186 #if $pg.quant_method.iso_labels.labeling == 'custom':
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	187 #for $l in $pg.quant_method.iso_labels.iso_label:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	188 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	189 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	190 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	191 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	192 @TMT2PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	193 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	194 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	195 @TMT6PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	196 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	197 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	198 @TMT8PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	199 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	200 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	201 @TMT10PLEX@
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	202 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	203 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	204 @TMT11PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	205 #end if
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	206 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	207 @TMTPRO16PLEX@
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	208 #end if
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	209 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	210 @ITRAQ4PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	211 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	212 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	213 @ITRAQ8PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	214 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	215 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	216 @IODOTMT6PLEX@
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	217 #end if
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	218 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	219 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms3':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	220 lcmsRunType: 'Reporter ion MS3'
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	221 reporterMassTolerance: 0.003
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	222 #if $pg.quant_method.filter_by_pif.filter_pif == 'True':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	223 reporterPif: ${pg.quant_method.filter_by_pif.reporter_pif}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	224 #else:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	225 reporterPif: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	226 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	227 reporterFraction: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	228 reporterBasePeakRatio: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	229 filterPif: ${pg.quant_method.filter_by_pif.filter_pif}
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	230 isobaricLabels:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	231 #if $pg.quant_method.iso_labels.labeling == 'custom':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	232 #for $l in $pg.quant_method.iso_labels.iso_label:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	233 - ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	234 #end for
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	235 #end if
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	236 #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	237 @TMT2PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	238 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	239 #if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	240 @TMT6PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	241 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	242 #if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	243 @TMT8PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	244 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	245 #if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	246 @TMT10PLEX@
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	247 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	248 #if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	249 @TMT11PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	250 #end if
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	251 #if $pg.quant_method.iso_labels.labeling == 'tmtpro16plex':
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	252 @TMTPRO16PLEX@
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	253 #end if
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	254 #if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	255 @ITRAQ4PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	256 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	257 #if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	258 @ITRAQ8PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	259 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	260 #if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	261 @IODOTMT6PLEX@
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	262 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	263 #end if
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	264 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	265 </configfile>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	266 <expand macro="ptxqc"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	267 </configfiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	268
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	269 <inputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	270 <section name="input_opts" title="Input Options" expanded="True">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	271 <param name="ftype" type="select" label="choose the type of your input files">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	272 <option value=".thermo.raw">thermo.raw</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	273 <option value=".mzxml">mzxml</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	274 <option value=".mzml">mzml</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	275 </param>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	276 <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	277 type="data" label="FASTA files"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	278 help="Specify one or more FASTA databases."/>
1 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="identifier_parse_rule" type="text"
8 ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	280 label="identifier parse rule" value=">([^\s]*)">
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	281 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	282 <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	283 <remove value="'"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	284 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	285 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	286 </param>
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="description_parse_rule" type="text"
8 ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	288 label="description parse rule" value=">(.*)"
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	289 help="Modify parse rules if needed.">
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	290 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	291 <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	292 <remove value="'"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	293 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	294 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	295 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	296 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	297
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	298 <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	299 <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	300 label="Specify an experimental design template (if needed). For detailed
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	301 instructions see the help text."/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	302 <param type="integer" name="min_peptide_len"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	303 label="minimum peptide length" value="7"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	304 help="Peptides shorter than this value will not be reported nor be considered during protein identification and quantification
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	305 short peptides are usually not unique in the protein database and therefore not statistically informative."/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	306 <param type="integer" name="max_peptide_mass"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	307 label="maximum peptide mass [Da]" value="4600"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	308 help="Peptides that are heavier than this mass will be discarded in the Andromeda search."/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	309 <param type="integer" name="min_unique_pep"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	310 label="minimum unique peptides" value="0"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	311 help="The minimum number of unique peptides a protein group should have to be considered as identified and reported in the final table."/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	312 <param name="calc_peak_properties" type="boolean" checked="false"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	313 label="Calculate peak properties"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	314 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	315 help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	316 <conditional name="mbr">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	317 <param name="match_between_runs" type="select"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	318 label="Match between runs"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	319 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs.">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	320 <option value="False" selected="true">No</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	321 <option value="True">Yes</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	322 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	323 <when value="False"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	324 <when value="True">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	325 <param name="matching_time_window" type="float" label="Match Time Window [min]" min="0" value="0.7"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	326 help="The time window that is used in 'Match between runs' for the transfer of identifications."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	327 <param name="matching_ion_mobility_window" type="float" label="Match Ion Mobility Window" min="0" value="0.05"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	328 help="The ion mobility window that is used in 'Match between runs' for the transfer of identifications."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	329 <param name="alignment_time_window" type="integer" label="Alignment Time Window [min]" min="0" value="20"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	330 help="The time window that is used in retention time alignment to search for the best alignment function."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	331 <param name="alignment_ion_mobility_window" type="integer" label="Alignment Ion Mobility" min="0" value="1"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	332 help="The ion mobility window that is used in ion mobility alignment to search for the best alignment function."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	333 <param name="match_unidentified_features" type="boolean" checked="false"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	334 label="Match unidentified Features"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	335 truevalue="True" falsevalue="False"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	336 help="Also unidentified peptide features will be matched between runs. Their expression profiles over multiple samples are written into the table called 'matchedFeatures.txt'."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	337 </when>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	338 </conditional>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	339 <param name="incl_contaminants" type="boolean" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	340 label="Include contaminants"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	341 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	342 help="‘Yes’ means that proteins from a contaminant list are automatically added to the list of proteins for in silico digestion (in the fasta file)"/>
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	343 <param name="decoy_mode" type="select"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	344 label="Decoy mode"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	345 help="The decoy sequences can be generated by reversing or randomizing the original protein sequences. Reversing is recommended.">
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	346 <option value="revert" selected="true">Revert</option>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	347 <option value="randomize">Randomize</option>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	348 </param>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	349 <param name="psm_fdr" type="float" label="PSM FDR" min="0" value="0.01"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	350 help="Specify the desired false discovery rate (FDR) at the peptide spectrum match (PSM) level. It is determined by the target-decoy approach. A value of 0.01 stands for 1% FDR."/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	351 <param name="protein_fdr" type="float" label="Protein FDR" min="0" value="0.01"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	352 help="Specify the desired false discovery rate (FDR) at the protein level. It is determined by the target-decoy approach. A value of 0.01 stands for 1% FDR."/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	353 <param name="min_pep_length" type="integer" label="Minimum peptide length for unspecific searches" min="1" value="8"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	354 help="During unspecific searches peptides that have fewer amino acids than this value will be discarded. This applies also to semi-specific (e.g. semi tryptic) searches"/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	355 <param name="max_pep_length" type="integer" label="Maximum peptide length for unspecific searches" min="1" value="25"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	356 help="During unspecific searches peptides that have more amino acids than this value will be discarded. This applies also to semi-specific (e.g. semi tryptic) searches"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	357 </section>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	358
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	359 <section name="protein_quant" title="Protein quantification" expanded="true">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	360
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	361 <param name="peptides_for_quantification" type="select" label="Peptides for quantification"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	362 help="Specify how the protein ratios will be calculated. When ‘All’ is selected the quantification is done on all peptides. With ‘Unique’, only the peptides unique for that specific protein group are used for quantification. The ‘unique + razor’ mode calculates protein ratios from the unique and razor peptides. Razor peptides are non-unique peptides assigned to the protein group with the most other peptides (Occam’s razor principle).">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	363 <option value="0">All</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	364 <option value="1" selected="true">Unique + razor</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	365 <option value="2">Unique</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	366 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	367
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	368 <conditional name="only_unmod_prot">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	369 <param name="unmod_prot" type="select"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	370 label="Use only unmodified peptides"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	371 help="Indicate here which kind of peptides should be used for protein quantification. If ‘No’, all peptides are used irrespective of their modification state. If ‘Yes’, all unmodified peptides are used plus those peptides that have only the modifications specified in the field below.">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	372 <option value="False">No</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	373 <option value="True" selected="true">Yes</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	374 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	375 <when value="True">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	376 <param name="mods_used_prot_quant" type="select" multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	377 label="Modifications used in protein quantification"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	378 help="Peptides containing only these modifications will be used for the quantification of proteins in addition to unmodified peptides. This includes ratio and intensity calculations including iBAQ">
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	379 <expand macro="default_mod_option" value="Oxidation (M)"/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	380 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	381 <expand macro="modification"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	382 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	383 <!-- note: the following default is different to the mquant default -->
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	384 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	385 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	386 help="If selected, also unmodified peptides will be discarded for which a modified counterpart has been identified with a modification that is not specified in the field above."/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	387 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	388 <when value="False">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	389 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	390 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	391
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	392 <section name="lfq_opts" title="LFQ Options" expanded="false">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	393 <param name="separateLfq" type="boolean" checked="false"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	394 label="Separate LFQ in parameter Groups"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	395 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	396 help="The MaxLFQ algorithm will be applied independently to samples in different parameter groups."/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	397 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	398 label="Stabilize large LFQ ratios"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	399 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	400 help="Large protein ratios will get an admixture of the total protein intensity ratio as described in the MaxLFQ paper"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	401 <param name="lfqRequireMsms" type="boolean" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	402 label="Require MS/MS for LFQ comparisons"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	403 truevalue="True" falsevalue="False"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	404 help="Requires for each pari-wise peptide intensity comparison that at least one of two peptides has been identified by MS/MS"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	405 <conditional name="do_ibaq">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	406 <param name="ibaq" type="select"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	407 label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	408 <option value="False">No</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	409 <option value="True">Yes</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	410 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	411 <when value="True">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	412 <param name="ibaqLogFit" type="boolean" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	413 label="Logarithmic fit"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	414 truevalue="True" falsevalue="False"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	415 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	416 <when value="False">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	417 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	418 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	419 <param name="advancedSiteIntensities" type="boolean" checked="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	420 label="Advanced site intensities"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	421 truevalue="True" falsevalue="False"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	422 </section>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	423
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	424 </section>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	425
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	426
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	427 <repeat name="paramGroups" title="Parameter Group" min="1" default="1">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	428 <param type="data" format="thermo.raw,mzXML,mzML" name="files" label="Infiles" multiple="true"
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	429 help="Only select infiles matching the filetype specified in the input options."/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	430 <param type="integer" name="maxMissedCleavages"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	431 label="missed cleavages" value="2"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	432 help="The number of missed cleavages that are maximally tolerated in the in-silico digestion of the protien sequences."/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	433 <param name="fixedModifications" type="select" label="fixed modifications"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	434 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	435 help="Select zero or more fixed modifications. They will always be attached to any occurence of the respective amino acid.">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	436 <expand macro="modification"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	437 <expand macro="default_mod_option" value="Carbamidomethyl (C)"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	438 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	439 <param name="variableModifications" type="select" label="variable modifications"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	440 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	441 help="Select zero or more variable modifications. Do not specify label modifications here, neither ms1 level labels, like SILAC, nor isobaric labels.">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	442 <expand macro="default_mod_option" value="Oxidation (M)"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	443 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	444 <expand macro="modification"/>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	445 </param>
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	446 <param name="enzymes" type="select" label="enzyme"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	447 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	448 help="Select zero or more enzymes. The enzymes used for generating the in silico peptides for the Andromeda search.">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	449 <expand macro="default_mod_option" value="Trypsin/P"/>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	450 <expand macro="proteases"/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	451 </param>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	452 <param name="digestion_mode" type="select" label="Digestion mode"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	453 help="'Unspecific means that no cleavage rule is applied but instead all peptides up to a maximal length are considered">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	454 <option value="0" selected="true">Specific</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	455 <option value="1">Semi-specific free N-terminus</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	456 <option value="2">Semi-specific free C-terminus</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	457 <option value="3">Semi-specific</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	458 <option value="4">Unspecific</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	459 <option value="5">No digestion</option>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	460 </param>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	461 <conditional name="quant_method">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	462 <param name="select_quant_method" type="select" label="Quantitation Methods"
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	463 help="Select a method if needed.">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	464 <option value="">None</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	465 <option value="lfq">label free quantification</option>
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	466 <option value="silac">label based quantification</option>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	467 <option value="reporter_ion_ms2">reporter ion MS2</option>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	468 <option value="reporter_ion_ms3">reporter ion MS3</option>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	469 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	470 <when value=""/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	471 <when value="silac">
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	472 <param name="light_labels" type="select" label="light labels"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	473 multiple="true" help="Select zero or more light modifications.">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	474 <expand macro="label"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	475 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	476 <param name="medium_labels" type="select" label="medium labels"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	477 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	478 help="Select zero modifications if you have two labels. Select a medium modification if you have three labels.">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	479 <expand macro="label"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	480 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	481 <param name="heavy_labels" type="select" label="heavy labels"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	482 multiple="true" help="Select zero or more heavy modifications.">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	483 <expand macro="label"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	484 </param>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	485 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	486 <when value="lfq">
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	487 <param type="integer" name="lfqMinRatioCount"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	488 label="LFQ minimum ratio count" value="2"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	489 help="Minimum number of peptides that has to be available in pair-wise comparisons between two samples for a protein."/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	490 <param type="integer" name="lfqMinEdgesPerNode"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	491 label="LFQ minimum number of neighbours" value="3"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	492 help="Defines the network to normalize the samples in the fast LFQ mode."/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	493 <param type="integer" name="lfqAvEdgesPerNode"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	494 label="LFQ average number of neighbours" value="6"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	495 help="Defines the network to normalize the samples in the fast LFQ mode."/>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	496 <param name="lfqNormType" type="select" label="Normalization type"
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	497 multiple="false" help="">
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	498 <option value="0">None</option>
13 181bd6a5f6ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ea679515491b0e9e13ec0084b59a40457eb355cc" galaxyp parents: 12 diff changeset	499 <option value="1" selected="true">Classic</option>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	500 </param>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	501 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	502 <when value="reporter_ion_ms2">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	503 <conditional name="iso_labels">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	504 <param name="labeling" type="select" label="isobaric labeling"
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	505 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	506 <option value="custom">custom</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	507 <option value="tmt2plex">TMT2plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	508 <option value="tmt6plex">TMT6plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	509 <option value="tmt8plex">TMT8plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	510 <option value="tmt10plex">TMT10plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	511 <option value="tmt11plex">TMT11plex</option>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	512 <option value="tmtpro16plex">TMTpro16plex</option>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	513 <option value="itraq4plex">iTRAQ4plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	514 <option value="itraq8plex">iTRAQ8plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	515 <option value="iodotmt6plex">iodoTMT6plex</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	516 </param>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	517 <when value="tmt2plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	518 <when value="tmt6plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	519 <when value="tmt8plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	520 <when value="tmt10plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	521 <when value="tmt11plex"/>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	522 <when value="tmtpro16plex"/>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	523 <when value="itraq4plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	524 <when value="itraq8plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	525 <when value="iodotmt6plex"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	526 <when value="custom">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	527 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	528 <param name="internallabel" type="select" label="internal label" help="contains Lys">
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	529 <expand macro="iso_labels"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	530 </param>
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	531 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	532 <option value="">None</option>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	533 <expand macro="iso_labels"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	534 </param>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	535 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	536 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	537 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	538 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	539 <param type="boolean" name="tmtlike" checked="false"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	540 label="TMT-like"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	541 truevalue="True" falsevalue="False"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	542 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	543 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	544 </conditional>
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	545 <conditional name="filter_by_pif">
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	546 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	547 truevalue="True" falsevalue="False"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	548 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	549 <when value="True">
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	550 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	551 max="1"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	552 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	553 </when>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	554 <when value="False"/>
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	555 </conditional>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	556 </when>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	557 <when value="reporter_ion_ms3">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	558 <conditional name="iso_labels">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	559 <param name="labeling" type="select" label="isobaric labeling"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	560 help="Select one of the standard labelings (correction factors are zero) or create a custom labeling.">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	561 <option value="custom">custom</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	562 <option value="tmt2plex">TMT2plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	563 <option value="tmt6plex">TMT6plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	564 <option value="tmt8plex">TMT8plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	565 <option value="tmt10plex">TMT10plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	566 <option value="tmt11plex">TMT11plex</option>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	567 <option value="tmtpro16plex">TMTpro16plex</option>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	568 <option value="itraq4plex">iTRAQ4plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	569 <option value="itraq8plex">iTRAQ8plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	570 <option value="iodotmt6plex">iodoTMT6plex</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	571 </param>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	572 <when value="tmt2plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	573 <when value="tmt6plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	574 <when value="tmt8plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	575 <when value="tmt10plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	576 <when value="tmt11plex"/>
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	577 <when value="tmtpro16plex"/>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	578 <when value="itraq4plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	579 <when value="itraq8plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	580 <when value="iodotmt6plex"/>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	581 <when value="custom">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	582 <repeat name="iso_label" title="Isobaric Label" min="1" default="1">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	583 <param name="internallabel" type="select" label="internal label" help="contains Lys">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	584 <expand macro="iso_labels"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	585 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	586 <param name="terminallabel" type="select" label="terminal label" help="contains Nter">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	587 <option value="">None</option>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	588 <expand macro="iso_labels"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	589 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	590 <param name="cm2" type="float" label="correction factor -2%" value="0.0"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	591 <param name="cm1" type="float" label="correction factor -1%" value="0.0"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	592 <param name="cp1" type="float" label="correction factor +1%" value="0.0"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	593 <param name="cp2" type="float" label="correction factor +2%" value="0.0"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	594 <param type="boolean" name="tmtlike" checked="false"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	595 label="TMT-like"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	596 truevalue="True" falsevalue="False"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	597 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	598 </when>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	599 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	600 <conditional name="filter_by_pif">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	601 <param name="filter_pif" type="boolean" checked="false" label="Filter by PIF"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	602 truevalue="True" falsevalue="False"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	603 help="If checked, quantified PSMs will be filtered by their precursor intensity fraction to avoid using peptides that clearly suffer from co-fragmentation with other peptide species."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	604 <when value="True">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	605 <param name="reporter_pif" type="float" label="Minimum reporter PIF" value="0.75" min="0"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	606 max="1"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	607 help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	608 </when>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	609 <when value="False"/>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	610 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	611 </when>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	612 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	613 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	614
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	615 <expand macro="ptxqc-opts"/>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	616
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	617 <section title="Output Options" name="output_opts" expanded="true">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	618 <param name="dry_run" type="boolean" checked="false"
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	619 label="Only create config files? (i.e. for testing)"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	620 truevalue="True" falsevalue=""/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	621 <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	622 multiple="true" optional="false">
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	623 <option value="proteinGroups">Protein Groups</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	624 <option value="mqpar">mqpar.xml</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	625 <option value="peptides">Peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	626 <option value="evidence">Evidence</option>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	627 <option value="parameters">Tabular Parameters</option>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	628 <option value="msms">MSMS</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	629 <option value="mzTab">mzTab</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	630 <option value="allPeptides">all peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	631 <option value="libraryMatch">library match</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	632 <option value="matchedFeatures">matched features</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	633 <option value="modificationSpecificPeptides">modification specific peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	634 <option value="ms3Scans">ms3 scans</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	635 <option value="msmsScans">msms scans</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	636 <option value="mzRange">mz range</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	637 <option value="peptideSection">peptide section</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	638 <option value="summary">summary</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	639 <option value="output_all">complete 'combined/txt/' directory (compressed)</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	640 <option value="log">MaxQuant and PTXQC log</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	641 <option value="config">yaml config file</option>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	642 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	643 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	644 </inputs>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	645
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	646 <expand macro="outputs"/>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	647
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	648 <tests>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	649 <!-- functional test with small mzXML file, no quantitation methods -->
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	650 <!-- Disable this test when initally testing as it takes avery long tome to run -->
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	651 <test expect_num_outputs="15">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	652 <param name="ftype" value=".mzxml" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	653 <param name="fasta_files" value="bsa.fasta" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	654 <param name="identifier_parse_rule" value=">([^\s]*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	655 <param name="description_parse_rule" value=">(.*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	656 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	657 <param name="files" value="BSA_min_23.mzXML"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	658 <param name="maxMissedCleavages" value="1"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	659 <param name="fixedModifications" value="Carbamidomethyl (C)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	660 <param name="variableModifications" value="Oxidation (M)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	661 <param name="enzymes" value="Trypsin/P" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	662 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	663 <param name="output" value="evidence,msms,allPeptides,msmsScans,mzTab,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all,config,mqpar" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	664 <output name="mqpar" file="01/mqpar.xml" lines_diff="6"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	665 <output name="evidence" file="01/combined/txt/evidence.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	666 <output name="msms" file="01/combined/txt/msms.txt" />
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	667 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	668 <output name="allPeptides" file="01/combined/txt/allPeptides.txt" lines_diff="2"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	669 <output name="msmsScans" file="01/combined/txt/msmsScans.txt" lines_diff="8"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	670 <output name="mzRange" file="01/combined/txt/mzRange.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	671 <output name="parameters" file="01/combined/txt/parameters.txt" lines_diff="10"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	672 <output name="peptides" file="01/combined/txt/peptides.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	673 <output name="peptideSection" file="01/combined/txt/peptideSection.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	674 <output name="proteinGroups" file="01/combined/txt/proteinGroups.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	675 <output name="summary" file="01/combined/txt/summary.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	676 <output name="modificationSpecificPeptides" file="01/combined/txt/modificationSpecificPeptides.txt" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	677 <output name="config" file="01/config.yml" lines_diff="2"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	678 </test>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	679 <!-- reporter ion ms2 + multiple param groups, testing yaml conf file and mqpar.xml only -->
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	680 <test expect_num_outputs="3">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	681 <param name="ftype" value=".mzxml" />
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	682 <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	683 <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	684 <param name="description_parse_rule" value=">(.*)" />
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	685 <param name="incl_contaminants" value="False" /> <!-- non-default value -->
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	686 <param name="min_pep_length" value="7" /> <!-- non-default value -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	687 <param name="max_pep_length" value="24" /> <!-- non-default value -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	688 <param name="decoy_mode" value="randomize" /> <!-- non-default value -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	689 <param name="psm_fdr" value="0.5" /> <!-- non-default value -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	690 <param name="protein_fdr" value="0.4" /> <!-- non-default value -->
6 2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	691 <section name="protein_quant">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	692 <param name="peptides_for_quantification" value="0"/><!-- non-default value -->
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	693 <conditional name="only_unmod_prot">
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	694 <param name="unmod_prot" value="True"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	695 <param name="mods_used_prot_quant" value="Pro5,Pro6"/>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	696 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c" galaxyp parents: 5 diff changeset	697 </section>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	698 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	699 <param name="files" value="BSA_min_23.mzXML"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	700 <param name="variableModifications" value="Oxidation (M)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	701 <param name="fixedModifications" value="" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	702 <conditional name="quant_method">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	703 <param name="select_quant_method" value="reporter_ion_ms2" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	704 <conditional name="iso_labels">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	705 <param name="labeling" value="custom" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	706 <repeat name="iso_label">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	707 <param name="internallabel" value="TMT2plex-Lys126" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	708 <param name="terminallabel" value="TMT2plex-Nter126" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	709 <param name="tmtlike" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	710 <param name="cp1" value="6.7" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	711 <param name="cp2" value="3" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	712 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	713 <repeat name="iso_label">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	714 <param name="internallabel" value="TMT2plex-Lys127" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	715 <param name="terminallabel" value="TMT2plex-Nter127" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	716 <param name="tmtlike" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	717 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	718 </conditional>
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	719 <conditional name="filter_by_pif">
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	720 <param name="filter_pif" value="False"/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	721 <param name="reporter_pif"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	722 value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	723 </conditional>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	724 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	725 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	726 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	727 <param name="files" value="BSA_min_22"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	728 <param name="variableModifications" value="" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	729 <param name="fixedModifications" value="" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	730 <param name="enzymes" value="" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	731 <conditional name="quant_method">
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	732 <param name="select_quant_method" value="reporter_ion_ms2"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	733 <conditional name="iso_labels">
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	734 <param name="labeling" value="itraq4plex"/>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	735 </conditional>
7 d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	736 <conditional name="filter_by_pif">
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	737 <param name="filter_pif" value="True"/>
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	738 <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used -->
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5" galaxyp parents: 6 diff changeset	739 </conditional>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	740 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	741 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	742 <param name="dry_run" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	743 <param name="output" value="config,mqpar,mzTab" />
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	744 <output name="config" file="02/config.yml" lines_diff="7" />
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	745 <!-- high difference due to unconsistant xml formatting in MQ -->
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	746 <output name="mqpar" file="02/mqpar.xml" lines_diff="24" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	747 </test>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	748 <!-- reporter ion ms3 + multiple param groups, testing yaml conf file and mqpar.xml only -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	749 <test expect_num_outputs="3">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	750 <param name="ftype" value=".mzxml" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	751 <param name="fasta_files" value="bsa.fasta" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	752 <param name="identifier_parse_rule" value=">([^\s]*)" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	753 <param name="description_parse_rule" value=">(.*)" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	754 <param name="incl_contaminants" value="False" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	755 <param name="min_pep_length" value="7" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	756 <param name="max_pep_length" value="24" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	757 <param name="decoy_mode" value="randomize" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	758 <param name="psm_fdr" value="0.5" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	759 <param name="protein_fdr" value="0.4" /> <!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	760 <section name="protein_quant">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	761 <param name="peptides_for_quantification" value="0"/><!-- non-default value -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	762 <conditional name="only_unmod_prot">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	763 <param name="unmod_prot" value="True"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	764 <param name="mods_used_prot_quant" value="Pro5,Pro6"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	765 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	766 </section>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	767 <repeat name="paramGroups">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	768 <param name="files" value="BSA_min_23.mzXML"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	769 <param name="variableModifications" value="Oxidation (M)" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	770 <param name="fixedModifications" value="" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	771 <conditional name="quant_method">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	772 <param name="select_quant_method" value="reporter_ion_ms3" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	773 <conditional name="iso_labels">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	774 <param name="labeling" value="custom" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	775 <repeat name="iso_label">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	776 <param name="internallabel" value="TMT2plex-Lys126" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	777 <param name="terminallabel" value="TMT2plex-Nter126" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	778 <param name="tmtlike" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	779 <param name="cp1" value="6.7" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	780 <param name="cp2" value="3" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	781 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	782 <repeat name="iso_label">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	783 <param name="internallabel" value="TMT2plex-Lys127" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	784 <param name="terminallabel" value="TMT2plex-Nter127" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	785 <param name="tmtlike" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	786 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	787 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	788 <conditional name="filter_by_pif">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	789 <param name="filter_pif" value="False"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	790 <param name="reporter_pif"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	791 value="0.6"/> <!-- as filter_pif is False this value will be ignored and 0 used instead -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	792 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	793 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	794 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	795 <repeat name="paramGroups">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	796 <param name="files" value="BSA_min_22"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	797 <param name="variableModifications" value="" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	798 <param name="fixedModifications" value="" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	799 <param name="enzymes" value="" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	800 <conditional name="quant_method">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	801 <param name="select_quant_method" value="reporter_ion_ms3"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	802 <conditional name="iso_labels">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	803 <param name="labeling" value="itraq4plex"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	804 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	805 <conditional name="filter_by_pif">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	806 <param name="filter_pif" value="True"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	807 <param name="reporter_pif" value="0.8"/> <!-- as filter_pif is True this value is used -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	808 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	809 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	810 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	811 <param name="dry_run" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	812 <param name="output" value="config,mqpar,mzTab" />
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	813 <output name="config" file="06/config.yml" lines_diff="7">
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	814 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	815 <has_text_matching expression="lcmsRunType\: \'Reporter ion MS3\'" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	816 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	817 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	818 <output name="mqpar" file="06/mqpar.xml" lines_diff="6">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	819 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	820 <has_text_matching expression=".lcmsRunType.Reporter ion MS3.\/lcmsRunType." />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	821 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	822 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	823 </test>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	824 <!-- lfq, testing yaml conf file and mqpar.xml only -->
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	825 <test expect_num_outputs="2">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	826 <param name="ftype" value=".mzxml" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	827 <param name="fasta_files" value="bsa.fasta" />
8 ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	828 <param name="identifier_parse_rule" value="^>.\\|(.)\\|.*$" />
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	829 <param name="description_parse_rule" value="^>.\\|.\\|[^ ]+ (.) OS.$" />
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	830 <param name="min_unique_pep" value="1" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	831 <param name="ibaq" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	832 <param name="ibaqLogFit" value="False" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	833 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	834 <param name="files" value="BSA_min_22"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	835 <param name="maxMissedCleavages" value="1"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	836 <param name="variableModifications" value="Oxidation (M)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	837 <conditional name="quant_method">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	838 <param name="select_quant_method" value="lfq" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	839 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	840 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	841 <param name="dry_run" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	842 <param name="output" value="config,mqpar" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	843 <output name="config" file="03/config.yml" lines_diff="2" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	844 <output name="mqpar" file="03/mqpar.xml" lines_diff="10" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	845 </test>
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	846 <!-- Test for MBR -->
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	847 <test expect_num_outputs="2">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	848 <param name="ftype" value=".mzxml" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	849 <param name="fasta_files" value="bsa.fasta" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	850 <param name="identifier_parse_rule" value="^>.\\|(.)\\|.*$" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	851 <param name="description_parse_rule" value="^>.\\|.\\|[^ ]+ (.) OS.$" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	852 <param name="min_unique_pep" value="1" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	853 <param name="ibaq" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	854 <param name="match_between_runs" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	855 <param name="ibaqLogFit" value="False" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	856 <repeat name="paramGroups">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	857 <param name="files" value="BSA_min_22"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	858 <param name="maxMissedCleavages" value="1"/>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	859 <param name="variableModifications" value="Oxidation (M)" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	860 <conditional name="quant_method">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	861 <param name="select_quant_method" value="lfq" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	862 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	863 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	864 <param name="dry_run" value="True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	865 <param name="output" value="config,mqpar" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	866 <output name="config" file="05/config.yml" lines_diff="2">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	867 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	868 <has_text_matching expression="matchBetweenRuns\: True" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	869 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	870 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	871 <output name="mqpar" file="05/mqpar.xml" lines_diff="4">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	872 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	873 <has_text_matching expression=".matchBetweenRuns.True.\/matchBetweenRuns." />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	874 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	875 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	876 </test>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	877 <!-- silac + fractions with experimental design template, testing yaml conf file and mqpar.xml only -->
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	878 <test expect_num_outputs="2">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	879 <param name="ftype" value=".mzxml" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	880 <param name="fasta_files" value="bsa.fasta" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	881 <param name="identifier_parse_rule" value=">([^\s]*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	882 <param name="description_parse_rule" value=">(.*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	883 <param name="template" value="04/exp_design" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	884 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	885 <param name="files" value="BSA_min_23.mzXML,BSA_min_22"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	886 <param name="fixedModifications" value="Carbamidomethyl (C)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	887 <param name="variableModifications" value="Oxidation (M)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	888 <param name="enzymes" value="Trypsin/P" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	889 <conditional name="quant_method">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	890 <param name="select_quant_method" value="silac" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	891 <param name="light_labels" value="Arg6,Lys4" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	892 <param name="heavy_labels" value="Arg10,DimethLys8" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	893 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	894 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	895 <param name="dry_run" value="True" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	896 <param name="output" value="config,mqpar" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	897 <output name="config" file="04/config.yml" lines_diff="2" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	898 <output name="mqpar" file="04/mqpar.xml" lines_diff="12" />
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	899 </test>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	900 <!-- PTXQC Test -->
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	901 <test expect_num_outputs="3">
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	902 <param name="ftype" value=".mzxml" />
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	903 <param name="fasta_files" value="tmt_data.fasta" />
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	904 <param name="identifier_parse_rule" value=">([^\s]*)" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	905 <param name="description_parse_rule" value=">(.*)" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	906 <repeat name="paramGroups">
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	907 <param name="files" value="tmt_data.mzXML"/>
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	908 <param name="variableModifications" value="Oxidation (M)" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	909 <param name="fixedModifications" value="" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	910 <conditional name="quant_method">
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	911 <param name="select_quant_method" value="reporter_ion_ms2" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	912 <conditional name="iso_labels">
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	913 <param name="labeling" value="tmt10plex" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	914 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	915 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	916 </repeat>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	917 <param name="do_it" value="True" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	918 <param name="output" value="config,mqpar" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	919 <output name="config" file="07/config.yml" lines_diff="2" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	920 <!-- high difference due to unconsistant xml formatting in MQ -->
12 0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	921 <output name="mqpar" file="07/mqpar.xml" lines_diff="4" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	922 <output name="ptxqc_report" file="07/combined/txt/report_v1.0.10_combined.pdf" compare="sim_size" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	923 </test>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	924 <!-- TMTpro16plex test -->
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	925 <test expect_num_outputs="3">
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	926 <param name="ftype" value=".mzxml" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	927 <param name="fasta_files" value="tmt_data_16.fasta" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	928 <param name="identifier_parse_rule" value=">([^\s]*)" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	929 <param name="description_parse_rule" value=">(.*)" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	930 <repeat name="paramGroups">
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	931 <param name="files" value="tmt_data.mzXML"/>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	932 <param name="variableModifications" value="Oxidation (M)" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	933 <param name="fixedModifications" value="" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	934 <conditional name="quant_method">
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	935 <param name="select_quant_method" value="reporter_ion_ms2" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	936 <conditional name="iso_labels">
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	937 <param name="labeling" value="tmtpro16plex" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	938 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	939 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	940 </repeat>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	941 <param name="do_it" value="False" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	942 <param name="output" value="config,mqpar,proteinGroups" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	943 <output name="config" file="08/config.yml" lines_diff="2" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	944 <!-- high difference due to unconsistant xml formatting in MQ -->
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	945 <output name="mqpar" file="08/mqpar.xml" lines_diff="24" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89" galaxyp parents: 11 diff changeset	946 <output name="proteinGroups" file="08/combined/txt/proteinGroups.txt" />
11 d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e" galaxyp parents: 10 diff changeset	947 </test>
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	948 </tests>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	949
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	950 <help><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	951 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	952
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	953 This tool is a wrapper for MaxQuant v@VERSION@. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	954
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	955 Input files
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	956
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	957 - Thermo raw, mzML, mzXMLfiles (in parameter group section)
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	958
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	959 - The datatype of all files has to be either 'thermo.raw', 'mzML' or 'mzXML'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
8 ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	960 - Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	961
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	962 ::
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	963
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	964 identifier parse rule description parse rule
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	965
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	966 Uniprot identifier >.\\|(.)\\| >.\\|.\\|[^ ]+ (.*) OS
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	967
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	968 NCBI accession >(gi\\|[0-9]*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	969
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	970 IPI accession >IPI:([^\\| .]*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	971
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	972 Everything after '>' >(.*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	973
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	974 Up to first space >([^ ]*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	975
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	976 Up to first tab character >([^\t]*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	977
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	978
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	979 - Optional files:
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	980
3 175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	981 - Tabular file with experimental design template:
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	982
3 175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	983 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template:
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	984
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	985 ::
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	986
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	987 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	988 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	989 File2 2 E1 False
3 175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	990 ghost 234 none
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	991 File3 3 E1 False
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	992 File4 E2 True
3 175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	993 File5 E1
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	994
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	995 - This is the counter-example with one error per line:
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	996
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	997 ::
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	998
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	999 Name Fraction Experiment PTM
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	1000 File1 1 E1 no (wrong PTM value)
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	1001 File2.mzxml 1 E2 (filename with extension)
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	1002 File3 f3 E1 (fraction not an integer)
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951" galaxyp parents: 1 diff changeset	1003 File4 1 (missing experiment)
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1004 (File5 missing)
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1005
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1006 Parameter Options
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1007
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1008 - Quantitation methods (in section parameter groups)
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1009
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1010 - label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1011 - label based: quantifies MS1 labelled samples ('SILAC', 'Dimethyl', 'ICAT', 'ICPL', 'mTRAQ', '18 O')
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1012
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1013 - for two channels: choose options from light and heavy sections
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1014 - for three channels: choose options from light, medium and heavy sections
10 f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e" galaxyp parents: 8 diff changeset	1015 - reporter ion ms2/ms3: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling
5 7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1016 - PTXQC quality control: quality control software creates an automatic quality control pdf report
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3" galaxyp parents: 4 diff changeset	1017
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1018
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1019 Output files
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1020
8 ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a" galaxyp parents: 7 diff changeset	1021 Different output file options are available, most of them are part of the MaxQuant txt directory.
1 8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847 galaxyp parents: 0 diff changeset	1022 ]]></help>
4 dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258" galaxyp parents: 3 diff changeset	1023 <expand macro="citations"/>
0 d4b6c9eae635 Initial commit. galaxyp parents: diff changeset	1024 </tool>

Mercurial > repos > galaxyp > maxquant

annotate maxquant.xml @ 14:e42225f8a659 draft