Mercurial > repos > galaxyp > maxquant

annotate maxquant.xml @ 15:97a7f34fcb6a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
author galaxyp
date Wed, 11 Aug 2021 09:24:23 +0000
parents e42225f8a659
children 74f5d355d156
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
209 #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex':
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
210 @TMTPRO18PLEX@
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
211 #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
212 #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
213 @ITRAQ4PLEX@
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 == 'itraq8plex':
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
216 @ITRAQ8PLEX@
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
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
218 #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
219 @IODOTMT6PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
220 #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
221 #end if
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.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
223 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
224 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
225 #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
226 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
227 #else:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
228 reporterPif: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
229 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
230 reporterFraction: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
231 reporterBasePeakRatio: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
232 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
233 isobaricLabels:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
234 #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
235 #for $l in $pg.quant_method.iso_labels.iso_label:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
236 - ['$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
237 #end for
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
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
239 #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
240 @TMT2PLEX@
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 == 'tmt6plex':
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
243 @TMT6PLEX@
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 == 'tmt8plex':
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
246 @TMT8PLEX@
10
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 == 'tmt10plex':
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
249 @TMT10PLEX@
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
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
251 #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
252 @TMT11PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
253 #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
254 #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
255 @TMTPRO16PLEX@
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
256 #end if
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
257 #if $pg.quant_method.iso_labels.labeling == 'tmtpro18plex':
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
258 @TMTPRO18PLEX@
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
259 #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
260 #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
261 @ITRAQ4PLEX@
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 #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
264 @ITRAQ8PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
265 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
266 #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
267 @IODOTMT6PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
268 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
269 #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
270 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
271 </configfile>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
272 <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
273 </configfiles>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
274
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
275 <inputs>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
276 <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
277 <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
278 <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
279 <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
280 <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
281 </param>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
282 <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
283 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
284 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
285 <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
286 label="identifier parse rule" value="&gt;([^\s]*)">
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
287 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
288 <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
289 <remove value="&apos;"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
290 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
291 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
292 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
293 <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
294 label="description parse rule" value="&gt;(.*)"
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
295 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
296 <sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
297 <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
298 <remove value="&apos;"/>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
299 </valid>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
300 </sanitizer>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
301 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
302 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
303
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
304 <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
305 <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
306 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
307 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
308 <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
309 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
310 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
311 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
312 <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
313 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
314 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
315 <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
316 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
317 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
318 <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
319 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
320 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
321 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
322 <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
323 <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
324 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
325 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
326 <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
327 <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
328 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
329 <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
330 <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
331 <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
332 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
333 <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
334 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
335 <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
336 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
337 <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
338 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
339 <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
340 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
341 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
342 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
343 </when>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
344 </conditional>
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
345 <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
346 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
347 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
348 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
349 <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
350 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
351 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
352 <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
353 <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
354 </param>
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="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
356 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
357 <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
358 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
359 <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
360 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
361 <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
362 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
363 </section>
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
364
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
365 <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
366
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
367 <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
368 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
369 <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
370 <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
371 <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
372 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
373
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
374 <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
375 <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
376 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
377 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
378 <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
379 <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
380 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
381 <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
382 <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
383 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
384 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
385 <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
386 <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
387 <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
388 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
389 <!-- 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
390 <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
391 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
392 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
393 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
394 <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
395 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
396 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
397
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
398 <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
399 <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
400 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
401 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
402 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
403 <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
404 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
405 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
406 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
407 <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
408 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
409 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
410 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
411 <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
412 <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
413 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
414 <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
415 <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
416 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
417 <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
418 <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
419 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
420 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
421 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
422 <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
423 </when>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
424 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
425 <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
426 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
427 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
428 </section>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
429
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
430 </section>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
431
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
432
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
433 <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
434 <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
435 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
436 <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
437 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
438 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
439 <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
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 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
442 <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
443 <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
444 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
445 <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
446 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
447 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
448 <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
449 <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
450 <expand macro="modification"/>
0
d4b6c9eae635 Initial commit.
galaxyp
parents:
diff changeset
451 </param>
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
452 <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
453 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
454 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
455 <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
456 <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
457 </param>
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
458 <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
459 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
460 <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
461 <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
462 <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
463 <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
464 <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
465 <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
466 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
467 <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
468 <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
469 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
470 <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
471 <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
472 <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
473 <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
474 <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
475 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
476 <when value=""/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
477 <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
478 <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
479 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
480 <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
481 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
482 <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
483 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
484 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
485 <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
486 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
487 <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
488 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
489 <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
490 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
491 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
492 <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
493 <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
494 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
495 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
496 <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
497 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
498 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
499 <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
500 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
501 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
502 <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
503 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
504 <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
505 <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
506 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
507 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
508 <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
509 <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
510 <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
511 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
512 <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
513 <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
514 <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
515 <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
516 <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
517 <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
518 <option value="tmtpro16plex">TMTpro16plex</option>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
519 <option value="tmtpro18plex">TMTpro18plex</option>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
520 <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
521 <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
522 <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
523 </param>
11
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="tmt2plex"/>
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="tmt6plex"/>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
526 <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
527 <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
528 <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
529 <when value="tmtpro16plex"/>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
530 <when value="tmtpro18plex"/>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
531 <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
532 <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
533 <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
534 <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
535 <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
536 <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
537 <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
538 </param>
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
539 <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
540 <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
541 <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
542 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
543 <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
544 <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
545 <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
546 <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
547 <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
548 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
549 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
550 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
551 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
552 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
553 <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
554 <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
555 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
556 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
557 <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
558 <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
559 max="1"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
560 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
561 </when>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
562 <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
563 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
564 </when>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
565 <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
566 <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
567 <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
568 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
569 <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
570 <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
571 <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
572 <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
573 <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
574 <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
575 <option value="tmtpro16plex">TMTpro16plex</option>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
576 <option value="tmtpro18plex">TMTpro18plex</option>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
577 <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
578 <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
579 <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
580 </param>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
581 <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
582 <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
583 <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
584 <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
585 <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
586 <when value="tmtpro16plex"/>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
587 <when value="tmtpro18plex"/>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
588 <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
589 <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
590 <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
591 <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
592 <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
593 <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
594 <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
595 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
596 <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
597 <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
598 <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
599 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
600 <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
601 <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
602 <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
603 <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
604 <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
605 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
606 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
607 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
608 </when>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
609 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
610 <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
611 <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
612 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
613 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
614 <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
615 <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
616 max="1"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
617 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
618 </when>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
619 <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
620 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
621 </when>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
622 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
623 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
624
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
625 <expand macro="ptxqc-opts"/>
0
d4b6c9eae635 Initial commit.
galaxyp
parents:
diff changeset
626
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
627 <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
628 <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
629 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
630 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
631 <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
632 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
633 <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
634 <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
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 <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
642 <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
643 <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
644 <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
645 <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
646 <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
647 <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
648 <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
649 <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
650 <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
651 <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
652 </param>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
653 </section>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
654 </inputs>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
655
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
656 <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
657
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
658 <tests>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
659 <!-- 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
660 <!-- 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
661 <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
662 <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
663 <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
664 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
665 <param name="description_parse_rule" value="&gt;(.*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
666 <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
667 <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
668 <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
669 <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
670 <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
671 <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
672 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
673 <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
674 <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
675 <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
676 <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
677 <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
678 <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
679 <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
680 <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
681 <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
682 <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
683 <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
684 <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
685 <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
686 <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
687 <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
688 </test>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
689 <!-- 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
690 <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
691 <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
692 <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
693 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
694 <param name="description_parse_rule" value="&gt;(.*)" />
6
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="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
696 <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
697 <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
698 <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
699 <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
700 <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
701 <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
702 <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
703 <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
704 <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
705 <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
706 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
707 </section>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
708 <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
709 <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
710 <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
711 <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
712 <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
713 <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
714 <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
715 <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
716 <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
717 <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
718 <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
719 <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
720 <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
721 <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
722 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
723 <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
724 <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
725 <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
726 <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
727 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
728 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
729 <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
730 <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
731 <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
732 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
733 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
734 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
735 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
736 <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
737 <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
738 <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
739 <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
740 <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
741 <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
742 <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
743 <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
744 <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
745 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
746 <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
747 <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
748 <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
749 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
750 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
751 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
752 <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
753 <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
754 <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
755 <!-- 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
756 <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
757 </test>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
758 <!-- 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
759 <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
760 <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
761 <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
762 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
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="description_parse_rule" value="&gt;(.*)" />
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="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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 <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
775 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
776 </section>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
777 <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
778 <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
779 <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
780 <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
781 <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
782 <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
783 <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
784 <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
785 <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
786 <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
787 <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
788 <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
789 <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
790 <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
791 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
792 <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
793 <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
794 <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
795 <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
796 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
797 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
798 <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
799 <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
800 <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
801 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
802 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
803 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
804 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
805 <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
806 <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
807 <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
808 <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
809 <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
810 <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
811 <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
812 <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
813 <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
814 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
815 <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
816 <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
817 <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
818 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
819 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
820 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
821 <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
822 <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
823 <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
824 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
825 <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
826 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
827 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
828 <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
829 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
830 <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
831 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
832 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
833 </test>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
834 <!-- 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
835 <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
836 <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
837 <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
838 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
839 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
840 <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
841 <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
842 <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
843 <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
844 <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
845 <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
846 <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
847 <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
848 <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
849 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
850 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
851 <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
852 <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
853 <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
854 <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
855 </test>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
856 <!-- 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
857 <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
858 <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
859 <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
860 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
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="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
862 <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
863 <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
864 <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
865 <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
866 <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
867 <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
868 <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
869 <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
870 <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
871 <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
872 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
873 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
874 <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
875 <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
876 <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
877 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
878 <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
879 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
880 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
881 <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
882 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
883 <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
884 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
885 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
886 </test>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
887 <!-- 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
888 <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
889 <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
890 <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
891 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
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="description_parse_rule" value="&gt;(.*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
893 <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
894 <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
895 <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
896 <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
897 <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
898 <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
899 <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
900 <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
901 <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
902 <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
903 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
904 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
905 <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
906 <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
907 <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
908 <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
909 </test>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
910 <!-- PTXQC Test -->
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
911 <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
912 <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
913 <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
914 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
915 <param name="description_parse_rule" value="&gt;(.*)" />
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
916 <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
917 <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
918 <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
919 <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
920 <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
921 <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
922 <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
923 <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
924 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
925 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
926 </repeat>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
927 <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
928 <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
929 <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
930 <!-- 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
931 <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
932 <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
933 </test>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
934 <!-- TMTpro16plex test -->
12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
935 <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
936 <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
937 <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
938 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
939 <param name="description_parse_rule" value="&gt;(.*)" />
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
940 <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
941 <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
942 <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
943 <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
944 <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
945 <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
946 <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
947 <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
948 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
949 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
950 </repeat>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
951 <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
952 <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
953 <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
954 <!-- 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
955 <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
956 <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
957 </test>
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
958 <!-- TMTpro18plex test -->
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
959 <test expect_num_outputs="2">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
960 <param name="ftype" value=".mzxml" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
961 <param name="fasta_files" value="tmt_data_18.fasta" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
962 <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
963 <param name="description_parse_rule" value="&gt;(.*)" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
964 <repeat name="paramGroups">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
965 <param name="files" value="tmt_data_18.mzXML"/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
966 <param name="variableModifications" value="Oxidation (M)" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
967 <param name="fixedModifications" value="" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
968 <conditional name="quant_method">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
969 <param name="select_quant_method" value="reporter_ion_ms2" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
970 <conditional name="iso_labels">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
971 <param name="labeling" value="tmtpro18plex" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
972 </conditional>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
973 </conditional>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
974 </repeat>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
975 <param name="do_it" value="False" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
976 <param name="output" value="msmsScans" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
977 <output name="msmsScans" file="09/combined/txt/msmsScans.txt">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
978 <assert_contents>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
979 <has_text text="GANDSMMM" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
980 </assert_contents>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
981 </output>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
982 </test>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
983 <!-- Thermo RAW file test -->
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
984 <test expect_num_outputs="2">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
985 <param name="ftype" value=".thermo.raw" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
986 <param name="fasta_files" value="bsa.fasta" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
987 <param name="identifier_parse_rule" value="^&gt;.*\|(.*)\|.*$" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
988 <param name="description_parse_rule" value="^&gt;.*\|.*\|[^ ]+ (.*) OS.*$" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
989 <param name="min_unique_pep" value="1" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
990 <repeat name="paramGroups">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
991 <param name="files" value="thermo.raw"/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
992 <param name="maxMissedCleavages" value="1"/>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
993 <param name="variableModifications" value="Oxidation (M)" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
994 <conditional name="quant_method">
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
995 <param name="select_quant_method" value="lfq" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
996 </conditional>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
997 </repeat>
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
998 <param name="output" value="config,mqpar" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
999 <output name="config" file="10/config.yml" lines_diff="2" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1000 <output name="mqpar" file="10/mqpar.xml" lines_diff="10" />
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1001 </test>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1002 </tests>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1003
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1004 <help><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1005 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
1006
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1007 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
1008
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1009 **Input files**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1010
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1011 - 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
1012
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1013 - 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
1014 - 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
1015
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1016 ::
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1017
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1018 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
1019
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1020 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
1021
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1022 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
1023
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1024 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
1025
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1026 Everything after '>' >(.*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1027
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1028 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
1029
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1030 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
1031
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1032
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1033 - 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
1034
3
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1035 - 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
1036
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1037 - 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. Thermo RAW files are handled differently (see table below). 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
1038
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1039 ::
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1040
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1041 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
1042 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
1043 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
1044 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
1045 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
1046 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
1047 File5 E1
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1048
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1049 - 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
1050
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1051 ::
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1052
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
1053 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
1054 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
1055 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
1056 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
1057 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
1058 (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
1059
15
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1060 - However, “.raw” (Thermo) is considered a part of the filename:
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1061
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1062 ::
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1063
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1064 Name Fraction Experiment PTM
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1065 File1.raw 1 E1 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1066 File2.raw 2 E1 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1067 File3.raw 3 E1 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1068 File4.raw 1 E2 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1069 File5.raw 2 E2 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1070 File6.raw 3 E2 False
97a7f34fcb6a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 641b1d3af3b589a861cde2dc2f8803c9b79df7be"
galaxyp
parents: 14
diff changeset
1071
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1072 **Parameter Options**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1073
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1074 - 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
1075
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1076 - 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
1077 - 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
1078
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1079 - 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
1080 - 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
1081 - 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
1082 - 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
1083
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1084
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1085 **Output files**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1086
8
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
1087 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
1088 ]]></help>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
1089 <expand macro="citations"/>
0
d4b6c9eae635 Initial commit.
galaxyp
parents:
diff changeset
1090 </tool>