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annotate maxquant.xml @ 12:0839f84def5e draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
author galaxyp
date Sun, 20 Jun 2021 16:37:41 +0000
parents d72c96ad9a16
children 181bd6a5f6ce
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12
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
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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
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2 <macros>
4
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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"
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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"
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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"
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6 </data>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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7 </xml>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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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"
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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"
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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"
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11 </data>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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12 </xml>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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13 <import>macros.xml</import>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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14 </macros>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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15 <expand macro="requirements"/>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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16 <command detect_errors="exit_code"><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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17 #import re
4
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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"
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19
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
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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"
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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"
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22 &&
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
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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"
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24 ## ==============================================================================================
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
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25
4
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26 #if 'config' in $output_opts.output:
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27 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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28 cp '$mq_conf' '$config'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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29 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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30 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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31 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles]
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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32 #set names_with_ext = [($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"
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33 #for $target, $link in zip($infiles, $names_with_ext)
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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34 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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35 ln -s '$target' '$link'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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36 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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37 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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38 python3 '$__tool_directory__/create_mqpar.py'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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39 #if $search_opts.template
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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40 --exp_design='$search_opts.template'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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41 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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42 --version=@VERSION@
1
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43 --num_threads=\${GALAXY_SLOTS:-1}
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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44 --substitution_rx='@SUBSTITUTION_RX@'
4
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45 --yaml='$mq_conf'
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46 mqpar.xml
1
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47
4
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48 #if $output_opts.dry_run:
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49 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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50 mkdir -p combined/txt
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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51 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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52 mv mqpar.xml combined/txt/mqpar.xml
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53 #else:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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54 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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55 maxquant mqpar.xml
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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56 #if 'log' in $output_opts.output:
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57 > '$log'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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58 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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59 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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60 mv mqpar.xml combined/txt/mqpar.xml
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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61 #if 'output_all' in $output_opts.output:
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62 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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63 tar -zcf '$output_all' ./combined/txt
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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64 #end if
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65
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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66 #if $qc.do_it:
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67 &&
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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68 Rscript '$qr' '$qr_yaml'
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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69 #if 'log' in $output_opts.output:
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70 >> '$log' 2>&1
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71 #end if
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72 &&
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
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73 cp './combined/txt/report_v@VERSION_PTXQC@_combined.pdf' '$ptxqc_report'
4
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74 #end if
0
d4b6c9eae635 Initial commit.
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75 #end if
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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76 ]]></command>
4
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77
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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78 <configfiles>
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79 <configfile name="mq_conf">
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80 #import re
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81 fastaFiles: [${input_opts.fasta_files}]
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82 parseRules:
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83 identifierParseRule: '${input_opts.identifier_parse_rule}'
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84 descriptionParseRule: '${input_opts.description_parse_rule}'
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85 minUniquePeptides: ${search_opts.min_unique_pep}
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86 minPepLen: ${search_opts.min_peptide_len}
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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87 maxPeptideMass: ${search_opts.max_peptide_mass}
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88 calcPeakProperties: ${search_opts.calc_peak_properties}
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89 #set writeMzTab = "mzTab" in $output_opts.output
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90 writeMzTab: $writeMzTab
6
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91 #if $protein_quant.lfq_opts.do_ibaq.ibaq == 'True':
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92 ibaq: ${protein_quant.lfq_opts.do_ibaq.ibaq}
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93 ibaqLogFit: ${protein_quant.lfq_opts.do_ibaq.ibaqLogFit}
4
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94 #end if
6
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95 separateLfq: ${protein_quant.lfq_opts.separateLfq}
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96 lfqStabilizeLargeRatios: ${protein_quant.lfq_opts.lfqStabilizeLargeRatios}
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97 lfqRequireMsms: ${protein_quant.lfq_opts.lfqRequireMsms}
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98 advancedSiteIntensities: ${protein_quant.lfq_opts.advancedSiteIntensities}
10
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99 matchBetweenRuns: ${search_opts.mbr.match_between_runs}
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100 #if $search_opts.mbr.match_between_runs == 'True':
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101 matchingTimeWindow: ${search_opts.mbr.matching_time_window}
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102 matchingIonMobilityWindow: ${search_opts.mbr.matching_ion_mobility_window}
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103 alignmentTimeWindow: ${search_opts.mbr.alignment_time_window}
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diff changeset
104 alignmentIonMobilityWindow: ${search_opts.mbr.alignment_ion_mobility_window}
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105 matchUnidentifiedFeatures: ${search_opts.mbr.match_unidentified_features}
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106 #end if
6
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107 includeContaminants: ${search_opts.incl_contaminants}
7
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108 minPeptideLengthForUnspecificSearch: ${search_opts.min_pep_length}
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109 maxPeptideLengthForUnspecificSearch: ${search_opts.max_pep_length}
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110 decoyMode: ${search_opts.decoy_mode}
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111 peptideFdr: ${search_opts.psm_fdr}
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112 proteinFdr: ${search_opts.protein_fdr}
6
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113 quantMode: ${protein_quant.peptides_for_quantification}
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114 restrictProteinQuantification: ${protein_quant.only_unmod_prot.unmod_prot}
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115 #if $protein_quant.only_unmod_prot.unmod_prot == 'True':
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diff changeset
116 #if $protein_quant.only_unmod_prot.mods_used_prot_quant:
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117 restrictMods: [${protein_quant.only_unmod_prot.mods_used_prot_quant}]
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118 #else:
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119 restrictMods: []
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120 #end if
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121 useCounterparts: $protein_quant.only_unmod_prot.discard_unmod_cpart_peptides
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122 #end if
4
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123 paramGroups:
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124 #for $pg in $paramGroups:
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125 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $pg.files]
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126 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
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127 - files: $names_with_ext
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128 maxMissedCleavages: ${pg.maxMissedCleavages}
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129 #if $pg.fixedModifications:
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130 fixedModifications: [${pg.fixedModifications}]
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131 #else:
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132 fixedModifications: []
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133 #end if
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diff changeset
134 #if $pg.variableModifications:
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135 variableModifications: [${pg.variableModifications}]
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136 #else:
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137 variableModifications: []
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138 #end if
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diff changeset
139 #if $pg.enzymes:
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140 enzymes: [${pg.enzymes}]
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diff changeset
141 #else:
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diff changeset
142 enzymes: []
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143 #end if
6
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144 enzymeMode: ${pg.digestion_mode}
4
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145 #if $pg.quant_method.select_quant_method == 'silac':
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146 labelMods:
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147 #if $pg.quant_method.light_labels:
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148 - [${pg.quant_method.light_labels}]
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149 #else:
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150 - []
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151 #end if
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152 #if $pg.quant_method.medium_labels:
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153 - [${pg.quant_method.medium_labels}]
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154 #else:
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155 - []
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156 #end if
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157 #if $pg.quant_method.heavy_labels:
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158 - [${pg.quant_method.heavy_labels}]
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159 #else:
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160 - []
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161 #end if
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162 #end if
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diff changeset
163 #if $pg.quant_method.select_quant_method == 'lfq':
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164 lfqMode: 1
12
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165 lfqNormType: ${pg.quant_method.lfqNormType}
4
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166 lfqMinEdgesPerNode: ${pg.quant_method.lfqMinEdgesPerNode}
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167 lfqAvEdgesPerNode: ${pg.quant_method.lfqAvEdgesPerNode}
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168 lfqMinRatioCount: ${pg.quant_method.lfqMinRatioCount}
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169 #end if
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170 #if $pg.quant_method.select_quant_method == 'reporter_ion_ms2':
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171 lcmsRunType: 'Reporter ion MS2'
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diff changeset
172 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
173 #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
174 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
175 #else:
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
176 reporterPif: 0
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
177 #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
178 reporterFraction: 0
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
179 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
180 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
181 isobaricLabels:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
182 #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
183 #for $l in $pg.quant_method.iso_labels.iso_label:
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
184 - ['$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
185 #end for
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
186 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
187 #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
188 @TMT2PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
189 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
190 #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
191 @TMT6PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
192 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
193 #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
194 @TMT8PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
195 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
196 #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
197 @TMT10PLEX@
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
198 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
199 #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
200 @TMT11PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
201 #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
202 #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
203 @TMTPRO16PLEX@
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
204 #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
205 #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
206 @ITRAQ4PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
207 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
208 #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
209 @ITRAQ8PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
210 #end if
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
211 #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
212 @IODOTMT6PLEX@
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
213 #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
214 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
215 #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
216 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
217 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
218 #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
219 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
220 #else:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
221 reporterPif: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
222 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
223 reporterFraction: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
224 reporterBasePeakRatio: 0
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
225 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
226 isobaricLabels:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
227 #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
228 #for $l in $pg.quant_method.iso_labels.iso_label:
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
229 - ['$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
230 #end for
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
231 #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
232 #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
233 @TMT2PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
234 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
235 #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
236 @TMT6PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
237 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
238 #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
239 @TMT8PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
240 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
241 #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
242 @TMT10PLEX@
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
243 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
244 #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
245 @TMT11PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
246 #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
247 #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
248 @TMTPRO16PLEX@
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
249 #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
250 #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
251 @ITRAQ4PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
252 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
253 #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
254 @ITRAQ8PLEX@
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
255 #end if
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
256 #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
257 @IODOTMT6PLEX@
10
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258 #end if
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259 #end if
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260 #end for
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261 </configfile>
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262 <expand macro="ptxqc"/>
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263 </configfiles>
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264
1
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265 <inputs>
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266 <section name="input_opts" title="Input Options" expanded="True">
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267 <param name="ftype" type="select" label="choose the type of your input files">
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268 <option value=".thermo.raw">thermo.raw</option>
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269 <option value=".mzxml">mzxml</option>
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270 <option value=".mzml">mzml</option>
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271 </param>
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272 <param format="fasta" multiple="true" name="fasta_files"
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273 type="data" label="FASTA files"
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274 help="Specify one or more FASTA databases."/>
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275 <param name="identifier_parse_rule" type="text"
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276 label="identifier parse rule" value="&gt;([^\s]*)">
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277 <sanitizer>
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278 <valid initial="string.printable">
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279 <remove value="&apos;"/>
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280 </valid>
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281 </sanitizer>
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282 </param>
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283 <param name="description_parse_rule" type="text"
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284 label="description parse rule" value="&gt;(.*)"
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285 help="Modify parse rules if needed.">
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286 <sanitizer>
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287 <valid initial="string.printable">
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288 <remove value="&apos;"/>
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289 </valid>
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290 </sanitizer>
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291 </param>
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292 </section>
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293
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294 <section name="search_opts" title="Search Options" expanded="true">
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295 <param format="tabular" name="template" type="data" optional="true"
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296 label="Specify an experimental design template (if needed). For detailed
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297 instructions see the help text."/>
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298 <param type="integer" name="min_peptide_len"
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299 label="minimum peptide length" value="7"
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300 help="Peptides shorter than this value will not be reported nor be considered during protein identification and quantification
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301 short peptides are usually not unique in the protein database and therefore not statistically informative."/>
1
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302 <param type="integer" name="max_peptide_mass"
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303 label="maximum peptide mass [Da]" value="4600"
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304 help="Peptides that are heavier than this mass will be discarded in the Andromeda search."/>
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305 <param type="integer" name="min_unique_pep"
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306 label="minimum unique peptides" value="0"
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307 help="The minimum number of unique peptides a protein group should have to be considered as identified and reported in the final table."/>
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308 <param name="calc_peak_properties" type="boolean" checked="false"
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309 label="Calculate peak properties"
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310 truevalue="True" falsevalue="False"
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311 help="If checked, several quantities characterizing peaks and isotopes patterns are calculated. This may lead to a substantial increase in computation time."/>
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312 <conditional name="mbr">
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313 <param name="match_between_runs" type="select"
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314 label="Match between runs"
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315 help="Identifications are transferred to non-sequenced or non-identified MS features in other LC-MS runs.">
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316 <option value="False" selected="true">No</option>
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317 <option value="True">Yes</option>
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318 </param>
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319 <when value="False"/>
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320 <when value="True">
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321 <param name="matching_time_window" type="float" label="Match Time Window [min]" min="0" value="0.7"
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322 help="The time window that is used in 'Match between runs' for the transfer of identifications."/>
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323 <param name="matching_ion_mobility_window" type="float" label="Match Ion Mobility Window" min="0" value="0.05"
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324 help="The ion mobility window that is used in 'Match between runs' for the transfer of identifications."/>
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325 <param name="alignment_time_window" type="integer" label="Alignment Time Window [min]" min="0" value="20"
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326 help="The time window that is used in retention time alignment to search for the best alignment function."/>
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327 <param name="alignment_ion_mobility_window" type="integer" label="Alignment Ion Mobility" min="0" value="1"
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328 help="The ion mobility window that is used in ion mobility alignment to search for the best alignment function."/>
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329 <param name="match_unidentified_features" type="boolean" checked="false"
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330 label="Match unidentified Features"
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331 truevalue="True" falsevalue="False"
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332 help="Also unidentified peptide features will be matched between runs. Their expression profiles over multiple samples are written into the table called 'matchedFeatures.txt'."/>
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333 </when>
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334 </conditional>
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335 <param name="incl_contaminants" type="boolean" checked="true"
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336 label="Include contaminants"
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337 truevalue="True" falsevalue="False"
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338 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)"/>
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339 <param name="decoy_mode" type="select"
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340 label="Decoy mode"
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341 help="The decoy sequences can be generated by reversing or randomizing the original protein sequences. Reversing is recommended.">
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342 <option value="revert" selected="true">Revert</option>
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343 <option value="randomize">Randomize</option>
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344 </param>
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345 <param name="psm_fdr" type="float" label="PSM FDR" min="0" value="0.01"
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346 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."/>
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347 <param name="protein_fdr" type="float" label="Protein FDR" min="0" value="0.01"
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348 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."/>
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349 <param name="min_pep_length" type="integer" label="Minimum peptide length for unspecific searches" min="1" value="8"
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350 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"/>
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351 <param name="max_pep_length" type="integer" label="Maximum peptide length for unspecific searches" min="1" value="25"
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352 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
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353 </section>
6
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354
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355 <section name="protein_quant" title="Protein quantification" expanded="true">
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356
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357 <param name="peptides_for_quantification" type="select" label="Peptides for quantification"
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358 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).">
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359 <option value="0">All</option>
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360 <option value="1" selected="true">Unique + razor</option>
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361 <option value="2">Unique</option>
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362 </param>
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363
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364 <conditional name="only_unmod_prot">
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365 <param name="unmod_prot" type="select"
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366 label="Use only unmodified peptides"
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367 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.">
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368 <option value="False">No</option>
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369 <option value="True" selected="true">Yes</option>
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370 </param>
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371 <when value="True">
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372 <param name="mods_used_prot_quant" type="select" multiple="true"
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373 label="Modifications used in protein quantification"
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374 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
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375 <expand macro="default_mod_option" value="Oxidation (M)"/>
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376 <expand macro="default_mod_option" value="Acetyl (Protein N-term)"/>
6
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377 <expand macro="modification"/>
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378 </param>
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379 <!-- note: the following default is different to the mquant default -->
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380 <param name="discard_unmod_cpart_peptides" type="boolean" label="Discard unmodified counterpart peptides" checked="true"
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381 truevalue="True" falsevalue="False"
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382 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."/>
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383 </when>
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384 <when value="False">
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385 </when>
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386 </conditional>
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387
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388 <section name="lfq_opts" title="LFQ Options" expanded="false">
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389 <param name="separateLfq" type="boolean" checked="false"
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390 label="Separate LFQ in parameter Groups"
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391 truevalue="True" falsevalue="False"
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392 help="The MaxLFQ algorithm will be applied independently to samples in different parameter groups."/>
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393 <param name="lfqStabilizeLargeRatios" type="boolean" checked="true"
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394 label="Stabilize large LFQ ratios"
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395 truevalue="True" falsevalue="False"
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396 help="Large protein ratios will get an admixture of the total protein intensity ratio as described in the MaxLFQ paper"/>
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397 <param name="lfqRequireMsms" type="boolean" checked="true"
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398 label="Require MS/MS for LFQ comparisons"
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399 truevalue="True" falsevalue="False"
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400 help="Requires for each pari-wise peptide intensity comparison that at least one of two peptides has been identified by MS/MS"/>
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401 <conditional name="do_ibaq">
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402 <param name="ibaq" type="select"
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403 label="iBAQ (calculates absolute protein abundances by normalizing to copy number and not protein mass)">
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404 <option value="False">No</option>
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405 <option value="True">Yes</option>
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406 </param>
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407 <when value="True">
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408 <param name="ibaqLogFit" type="boolean" checked="true"
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409 label="Logarithmic fit"
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410 truevalue="True" falsevalue="False"/>
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411 </when>
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412 <when value="False">
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413 </when>
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414 </conditional>
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415 <param name="advancedSiteIntensities" type="boolean" checked="true"
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416 label="Advanced site intensities"
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417 truevalue="True" falsevalue="False"/>
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418 </section>
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419
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420 </section>
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421
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422
4
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diff changeset
423 <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
424 <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
425 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
426 <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
427 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
428 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
429 <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
430 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
431 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
432 <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
433 <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
434 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
435 <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
436 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
437 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
438 <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
439 <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
440 <expand macro="modification"/>
0
d4b6c9eae635 Initial commit.
galaxyp
parents:
diff changeset
441 </param>
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
442 <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
443 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
444 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
445 <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
446 <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
447 </param>
6
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
448 <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
449 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
450 <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
451 <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
452 <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
453 <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
454 <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
455 <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
456 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
457
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
458 <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
459 <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
460 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
461 <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
462 <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
463 <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
464 <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
465 <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
466 </param>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
467 <when value=""/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
468 <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
469 <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
470 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
471 <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
472 </param>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
473 <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
474 multiple="true"
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
475 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
476 <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
477 </param>
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="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
479 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
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>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
482 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
483 <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
484 <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
485 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
486 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
487 <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
488 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
489 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
490 <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
491 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
492 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
493 <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
494 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
495 <option value="0">None</option>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
496 <option value="1">Classic</option>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
497 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
498 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
499 <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
500 <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
501 <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
502 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
503 <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
504 <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
505 <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
506 <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
507 <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
508 <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
509 <option value="tmtpro16plex">TMTpro16plex</option>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
510 <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
511 <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
512 <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
513 </param>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
514 <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
515 <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
516 <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
517 <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
518 <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
519 <when value="tmtpro16plex"/>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
520 <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
521 <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
522 <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
523 <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
524 <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
525 <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
526 <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
527 </param>
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
528 <param name="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
529 <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
530 <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
531 </param>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
532 <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
533 <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
534 <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
535 <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
536 <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
537 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
538 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
539 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
540 </when>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
541 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
542 <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
543 <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
544 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
545 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
546 <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
547 <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
548 max="1"
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
549 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
550 </when>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
551 <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
552 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
553 </when>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
554 <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
555 <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
556 <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
557 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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 <option value="tmtpro16plex">TMTpro16plex</option>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
565 <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
566 <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
567 <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
568 </param>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
569 <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
570 <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
571 <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
572 <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
573 <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
574 <when value="tmtpro16plex"/>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
575 <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
576 <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
577 <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
578 <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
579 <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
580 <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
581 <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
582 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
583 <param name="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
584 <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
585 <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
586 </param>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
587 <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
588 <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
589 <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
590 <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
591 <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
592 label="TMT-like"
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diff changeset
593 truevalue="True" falsevalue="False"/>
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diff changeset
594 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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parents: 8
diff changeset
595 </when>
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parents: 8
diff changeset
596 </conditional>
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diff changeset
597 <conditional name="filter_by_pif">
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diff changeset
598 <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"
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diff changeset
599 truevalue="True" falsevalue="False"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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diff changeset
600 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"
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parents: 8
diff changeset
601 <when value="True">
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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diff changeset
602 <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"
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parents: 8
diff changeset
603 max="1"
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
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parents: 8
diff changeset
604 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"
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parents: 8
diff changeset
605 </when>
11
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parents: 10
diff changeset
606 <when value="False"/>
10
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parents: 8
diff changeset
607 </conditional>
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parents: 8
diff changeset
608 </when>
4
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parents: 3
diff changeset
609 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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parents: 3
diff changeset
610 </repeat>
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diff changeset
611
6
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parents: 5
diff changeset
612 <expand macro="ptxqc-opts"/>
0
d4b6c9eae635 Initial commit.
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parents:
diff changeset
613
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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parents: 0
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614 <section title="Output Options" name="output_opts" expanded="true">
4
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615 <param name="dry_run" type="boolean" checked="false"
6
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diff changeset
616 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"
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diff changeset
617 truevalue="True" falsevalue=""/>
1
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parents: 0
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618 <param type="select" name="output" label="Select the desired outputs."
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619 multiple="true" optional="false">
4
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620 <option value="proteinGroups">Protein Groups</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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621 <option value="mqpar">mqpar.xml</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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622 <option value="peptides">Peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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623 <option value="evidence">Evidence</option>
11
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diff changeset
624 <option value="parameters">Tabular Parameters</option>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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625 <option value="msms">MSMS</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
626 <option value="mzTab">mzTab</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
627 <option value="allPeptides">all peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
628 <option value="libraryMatch">library match</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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parents: 3
diff changeset
629 <option value="matchedFeatures">matched features</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
630 <option value="modificationSpecificPeptides">modification specific peptides</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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631 <option value="ms3Scans">ms3 scans</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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632 <option value="msmsScans">msms scans</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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633 <option value="mzRange">mz range</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
634 <option value="peptideSection">peptide section</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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635 <option value="summary">summary</option>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
636 <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"
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diff changeset
637 <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"
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638 <option value="config">yaml config file</option>
1
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639 </param>
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diff changeset
640 </section>
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641 </inputs>
4
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diff changeset
642
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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parents: 3
diff changeset
643 <expand macro="outputs"/>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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parents: 0
diff changeset
644
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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parents: 0
diff changeset
645 <tests>
4
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diff changeset
646 <!-- functional test with small mzXML file, no quantitation methods -->
6
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diff changeset
647 <!-- 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"
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diff changeset
648 <test expect_num_outputs="15">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
649 <param name="ftype" value=".mzxml" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
650 <param name="fasta_files" value="bsa.fasta" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
651 <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"
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diff changeset
652 <param name="description_parse_rule" value="&gt;(.*)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
653 <repeat name="paramGroups">
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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654 <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"
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diff changeset
655 <param name="maxMissedCleavages" value="1"/>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
656 <param name="fixedModifications" value="Carbamidomethyl (C)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
657 <param name="variableModifications" value="Oxidation (M)" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
658 <param name="enzymes" value="Trypsin/P" />
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
659 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
660 <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"
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661 <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"
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diff changeset
662 <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"
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parents: 3
diff changeset
663 <output name="msms" file="01/combined/txt/msms.txt" />
12
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diff changeset
664 <output name="mzTab" file="01/combined/txt/mzTab.mzTab" lines_diff="34"/>
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diff changeset
665 <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"
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diff changeset
666 <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"
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667 <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"
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diff changeset
668 <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"
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diff changeset
669 <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"
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diff changeset
670 <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"
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diff changeset
671 <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"
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672 <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"
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diff changeset
673 <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"
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parents: 3
diff changeset
674 <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"
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diff changeset
675 </test>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
676 <!-- 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"
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parents: 3
diff changeset
677 <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
678 <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
679 <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
680 <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
681 <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
682 <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
683 <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
684 <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
685 <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
686 <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
687 <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
688 <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
689 <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
690 <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
691 <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
692 <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
693 </conditional>
2133b0be850a "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 4e77eeda8a112fb50af00325a5164b986c16fc5c"
galaxyp
parents: 5
diff changeset
694 </section>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
695 <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
696 <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
697 <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
698 <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
699 <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
700 <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
701 <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
702 <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
703 <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
704 <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
705 <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
706 <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
707 <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
708 <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
709 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
710 <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
711 <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
712 <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
713 <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
714 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
715 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
716 <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
717 <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
718 <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
719 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
720 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
721 </conditional>
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="paramGroups">
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="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
725 <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
726 <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
727 <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
728 <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
729 <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
730 <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
731 <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
732 </conditional>
7
d253b379322b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit f63ff6d5d0c44012a17e87293811765951655bd5"
galaxyp
parents: 6
diff changeset
733 <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
734 <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
735 <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
736 </conditional>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
737 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
738 </repeat>
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="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
740 <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
741 <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
742 <!-- 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
743 <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
744 </test>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
745 <!-- 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
746 <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
747 <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
748 <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
749 <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
750 <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
751 <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
752 <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
753 <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
754 <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
755 <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
756 <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
757 <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
758 <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
759 <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
760 <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
761 <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
762 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
763 </section>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
764 <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
765 <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
766 <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
767 <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
768 <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
769 <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
770 <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
771 <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
772 <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
773 <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
774 <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
775 <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
776 <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
777 <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
778 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
779 <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
780 <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
781 <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
782 <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
783 </repeat>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
784 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
785 <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
786 <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
787 <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
788 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
789 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
790 </conditional>
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="paramGroups">
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="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
794 <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
795 <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
796 <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
797 <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
798 <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
799 <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
800 <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
801 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
802 <conditional name="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
803 <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
804 <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
805 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
806 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
807 </repeat>
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="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
809 <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
810 <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
811 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
812 <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
813 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
814 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
815 <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
816 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
817 <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
818 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
819 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
820 </test>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
821 <!-- 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
822 <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
823 <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
824 <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
825 <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
826 <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
827 <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
828 <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
829 <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
830 <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
831 <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
832 <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
833 <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
834 <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
835 <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
836 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
837 </repeat>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
838 <param name="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
839 <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
840 <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
841 <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
842 </test>
10
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
843 <!-- 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
844 <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
845 <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
846 <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
847 <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
848 <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
849 <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
850 <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
851 <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
852 <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
853 <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
854 <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
855 <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
856 <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
857 <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
858 <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
859 </conditional>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
860 </repeat>
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="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
862 <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
863 <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
864 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
865 <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
866 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
867 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
868 <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
869 <assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
870 <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
871 </assert_contents>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
872 </output>
f522c08e900c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 63e45d43f403514ab0ceafaf441d761866f1eb7e"
galaxyp
parents: 8
diff changeset
873 </test>
4
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
874 <!-- 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
875 <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
876 <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
877 <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
878 <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
879 <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
880 <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
881 <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
882 <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
883 <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
884 <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
885 <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
886 <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
887 <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
888 <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
889 <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
890 </conditional>
dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 3
diff changeset
891 </repeat>
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="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
893 <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
894 <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
895 <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
896 </test>
11
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
897 <!-- PTXQC Test -->
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
898 <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
899 <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
900 <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
901 <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
902 <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
903 <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
904 <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
905 <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
906 <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
907 <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
908 <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
909 <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
910 <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
911 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
912 </conditional>
d72c96ad9a16 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
galaxyp
parents: 10
diff changeset
913 </repeat>
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="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
915 <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
916 <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
917 <!-- 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
918 <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
919 <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
920 </test>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
921 <!-- TMTpro16plex test -->
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
922 <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
923 <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
924 <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
925 <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
926 <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
927 <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
928 <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
929 <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
930 <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
931 <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
932 <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
933 <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
934 <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
935 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
936 </conditional>
0839f84def5e "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit d0dc9303d449c63a6ffe8fbfe195951d5db9cb89"
galaxyp
parents: 11
diff changeset
937 </repeat>
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="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
939 <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
940 <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
941 <!-- 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
942 <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
943 <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
944 </test>
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
945 </tests>
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
946
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
947 <help><![CDATA[
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
948 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
949
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
950 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
951
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
952 **Input files**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
953
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
954 - 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
955
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
956 - 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
957 - 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
958
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
959 ::
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
960
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
961 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
962
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
963 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
964
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
965 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
966
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
967 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
968
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
969 Everything after '>' >(.*)
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
970
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
971 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
972
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
973 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
974
ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
galaxyp
parents: 7
diff changeset
975
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
976 - 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
977
3
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
978 - 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
979
3
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
980 - Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. This is a (syntactically) correct experimental design template:
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
981
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
982 ::
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
983
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
984 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
985 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
986 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
987 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
988 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
989 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
990 File5 E1
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
991
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
992 - 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
993
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
994 ::
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
995
175e062b6a17 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
galaxyp
parents: 1
diff changeset
996 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
997 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
998 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
999 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
1000 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
1001 (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
1002
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1003 **Parameter Options**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1004
5
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1005 - 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
1006
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1007 - 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
1008 - 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
1009
7f432d87c82c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit dad20a951ffa71a4b98fd851e496b50cd423e0a3"
galaxyp
parents: 4
diff changeset
1010 - 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
1011 - 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
1012 - 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
1013 - 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
1014
1
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1015
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents: 0
diff changeset
1016 **Output files**
8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1017
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ea0a1d50c83f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 72cbf6fcc4930abe5da8e895a2b35951a63e881a"
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1018 Different output file options are available, most of them are part of the MaxQuant txt directory.
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8bac3cc5c5de planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1019 ]]></help>
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dcd39bcc7481 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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1020 <expand macro="citations"/>
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d4b6c9eae635 Initial commit.
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1021 </tool>