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annotate lcmsmatching.xml @ 6:b8f70d8216b3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
author prog
date Mon, 27 Mar 2017 06:27:29 -0400
parents 18254e8d1b72
children 882f2f20028b
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1 <tool id="lcmsmatching" name="LC/MS matching" version="3.3.0" profile="16.01">
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2
1
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3 <description>Annotation of MS peaks using matching on a spectra database.</description>
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5 <requirements>
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6 <!--<requirement type="package" version="3.3.3">r</requirement>-->
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7 <requirement type="package" version="7.0">readline</requirement> <!-- Try readline 7.0 -->
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8 <requirement type="package" version="1.20.0">r-getopt</requirement>
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9 <requirement type="package" version="1.0.0">r-stringr</requirement>
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10 <requirement type="package" version="1.8.3">r-plyr</requirement>
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11 <requirement type="package" version="3.98">r-xml</requirement>
1
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12 <requirement type="package" version="1.0_6">r-bitops</requirement>
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13 <requirement type="package" version="1.95">r-rcurl</requirement>
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14 <requirement type="package" version="1.1">r-jsonlite</requirement>
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15 </requirements>
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1
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17 <code file="list-chrom-cols.py"/>
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18 <code file="list-file-cols.py"/>
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19 <code file="list-ms-mode-values.py"/>
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21 <!--=======
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22 = COMMAND =
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23 ========-->
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1
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25 <command>
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26 <![CDATA[
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27 ## @@@BEGIN_CHEETAH@@@
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28 $__tool_directory__/search-mz
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29
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30 ## Input file
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31 -i "$mzrtinput"
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32 --input-col-names "mz=$inputmzfield,rt=$inputrtfield"
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33 --rtunit "$inputrtunit"
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35 ## Database
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36 #if $db.dbtype == "inhouse"
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37 -d file
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38 --db-fields "mztheo=$db.dbmzreffield,chromcolrt=$db.dbchromcolrtfield,compoundid=$db.dbspectrumidfield,chromcol=$db.dbchromcolfield,msmode=$db.dbmsmodefield,peakattr=$db.dbpeakattrfield,pubchemcompid=$db.dbpubchemcompidfield,chebiid=$db.dbchebiidfield,hmdbid=$db.dbhmdbidfield,keggid=$db.dbkeggidfield"
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39 --db-ms-modes "pos=$db.dbmsposmode,neg=$db.dbmsnegmode"
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40 --db-rt-unit $db.dbrtunit
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41 #end if
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42 #if $db.dbtype == "peakforest"
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43 -d peakforest
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44 --db-token "$db.dbtoken"
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45 #end if
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46 --url "$db.dburl"
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47
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48 ## M/Z matching
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49 -m $mzmode -p $mzprec -s $mzshift
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50
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51 ## Precursor matching
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52 #if $prec.match == "true"
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53 --precursor-match --pos-prec "$prec.pos" --neg-prec "$prec.neg"
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54 #end if
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55 #if $prec.match == "true" and $chromcols:
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56 --precursor-rt-tol $tolz
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57 #end if
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58
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59 ## Chromatographic columns options and retention matching
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60 #if $chromcols:
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61 -c "$chromcols" --check-cols --rttolx $tolx --rttoly $toly
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62 #end if
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63
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64 ## Table outputs
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65 -o "$mainoutput" --peak-output-file "$peaksoutput" --same-rows --same-cols
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66
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67 ## HTML output
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68 --html-output-file "$htmloutput" --no-main-table-in-html-output
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69
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70 ## Ouput setting
6
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71 --molids-sep "$molidssep"
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72 ## @@@END_CHEETAH@@@
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73 ]]></command>
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74
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75 <!--======
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76 = INPUTS =
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77 =======-->
0
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78
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79 <inputs>
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80
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81 <!-- DATABASE -->
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82
1
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83 <conditional name="db">
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84
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85 <param name="dbtype" label="Database" type="select" refresh_on_change="true">
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86 <option value="inhouse">In-house</option>
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87 <option value="peakforest">Peakforest</option>
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88 </param>
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89
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90 <when value="inhouse">
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91 <!-- Database file -->
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92 <param name="dburl" label="Database file" type="data" format="tabular,tsv" refresh_on_change="true" help="Decimal: '.', missing: NA, mode: character and numerical, sep: tabular. Retention time values must be in seconds."/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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93
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94 <!-- File database field names -->
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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95 <param name="dbspectrumidfield" type="select" label="Database file Spectrum ID column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'spectrumid,accession,compoundid,molid')" help="Select the Spectrum ID column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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96 <param name="dbmzreffield" type="select" label="Database file Reference MZ column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'mztheo,mzexp,mz')" help="Select the Reference MZ column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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97 <param name="dbchromcolfield" type="select" label="Database file Chromatographic Column Name column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'chromcol,col')" help="Select the Chromatographic Column Name column of the database file." refresh_on_change="true"/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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98 <param name="dbchromcolrtfield" type="select" label="Database file Chromatographic Column Retention Time column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'chromcolrt,colrt,rt')" help="Select the Chromatographic Column Retention Time column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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99 <param name="dbmsmodefield" type="select" label="Database file MS Mode column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'msmode,mode')" help="Select the MS Mode column of the database file." refresh_on_change="true"/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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100 <param name="dbpeakattrfield" type="select" label="Database file Peak Attribution column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'peakattr,attr')" help="Select the Peak Attribution column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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101 <param name="dbpubchemcompidfield" type="select" label="Database file PubChem Compound ID column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'pubchemcompid,pubchemid,pubchemcomp,pubchem')" help="Select the PubChem Compound ID column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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102 <param name="dbchebiidfield" type="select" label="Database file ChEBI ID column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'chebiid,chebi')" help="Select the ChEBI ID column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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103 <param name="dbhmdbidfield" type="select" label="Database file HMDB Metabolite ID column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'hmdbid,hmdb')" help="Select the HMDB Metabolite ID column of the database file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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104 <param name="dbkeggidfield" type="select" label="Database file KEGG Compound ID column name" dynamic_options="get_file_cols(file = db['dburl'], preferred = 'keggid,kegg')" help="Select the KEGG Compound ID column of the database file."/>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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105
1
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106 <!-- File database MS modes -->
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107 <param name="dbmsposmode" label="File database MS Positive mode" type="select" dynamic_options="get_ms_mode_value(file = db['dburl'], col = db['dbmsmodefield'], preferred = 'POS,pos,+')" help="Select the value used to identify the positive MS mode."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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108 <param name="dbmsnegmode" label="File database MS Negative mode" type="select" dynamic_options="get_ms_mode_value(file = db['dburl'], col = db['dbmsmodefield'], preferred = 'NEG,neg,-')" help="Select the value used to identify the negitive MS mode."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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109
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110 <!-- File database RT unit -->
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111 <param name="dbrtunit" label="Retention time unit" type="select" display="radio" multiple="false" help="">
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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112 <option value="sec">Seconds</option>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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113 <option value="min">Minutes</option>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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114 </param>
1
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115
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116 <param name="dbtoken" type="text" size="32" value="" hidden="true"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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117 </when>
0
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118
1
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119 <when value="peakforest">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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120 <param name="dburl" type="text" size="128" value="https://peakforest-alpha.inra.fr/rest" refresh_on_change="true"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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121
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122 <param name="dbtoken" label="Peakforest security token" type="text" size="32" value="" refresh_on_change="true" help="If you do not have yet a Peakforest token, go to Peakforest website and request one from your account."/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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123
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124 <param name="dbfields" type="text" size="32" value="" hidden="true"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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125 </when>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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126 </conditional>
0
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127
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128 <!-- INPUT -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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129
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130 <!-- Input file -->
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b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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131 <param name="mzrtinput" label="Input file - MZ(/RT) values" type="data" format="tabular,tsv" refresh_on_change="true" help="Decimal: '.', missing: NA, mode: character and numerical, sep: tabular. RT values must be in seconds."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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132
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133 <!-- Input field field names -->
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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134 <param name="inputmzfield" type="select" label="Input file MZ column name" dynamic_options="get_file_cols(file = mzrtinput, preferred = 'mzmed,mz')" help="Select the MZ column of the input file."/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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135 <param name="inputrtfield" type="select" label="Input file RT column name" dynamic_options="get_file_cols(file = mzrtinput, preferred = 'rtmed,rt')" help="Select the RT column of the input file."/>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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136
6
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137 <!-- Input file RT unit -->
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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138 <param name="inputrtunit" label="Retention time unit" type="select" display="radio" multiple="false" help="">
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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139 <option value="sec">Seconds</option>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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140 <option value="min">Minutes</option>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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141 </param>
0
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142
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143 <!-- M/Z MATCHING -->
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144
1
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145 <!-- Mode -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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146 <param name="mzmode" label="MS mode" type="select" display="radio" multiple="false" help="">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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147 <option value="pos">Positive</option>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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148 <option value="neg">Negative</option>
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149 </param>
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150
1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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151 <!-- MZ matching parameters -->
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152 <param name="mzprec" label="M/Z precision (in ppm)" type="float" help="" value="5"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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153 <param name="mzshift" label="M/Z shift (in ppm)" type="float" help="" value="0"/>
0
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154
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155 <!-- RETENTION TIME PARAMETERS -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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156
1
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157 <!-- List of chromatographic columns -->
6
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158 <param name="chromcols" type="select" label="Chromatographic columns" multiple="true" dynamic_options="get_chrom_cols(dbtype = db['dbtype'], dburl = db['dburl'], dbtoken = db['dbtoken'], col_field = db['dbchromcolfield'])" help="Select here the set of chromatographic columns against which the retention time matching will be run."/>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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159
1
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160 <!-- Tolerances -->
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161 <param name="tolx" label="RTX retention time tolerance, parameter x (in seconds)" type="float" help="" value="5"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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162 <param name="toly" label="RTY retention time tolerance, parameter y" type="float" help="" value="0.8"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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163 <param name="tolz" label="RTZ retention time tolerance, used when precursor matching is enabled." type="float" help="" value="5"/>
0
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164
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165 <!-- PRECURSOR MATCH -->
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166 <conditional name="prec">
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167
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168 <param name="match" label="Precursor match" type="select">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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169 <option value="false">Off</option>
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170 <option value="true">On</option>
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171 </param>
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172
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173 <when value="false"></when>
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174 <when value="true">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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175 <!-- Negative precursors -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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176 <param name="neg" label="List of negative precursors" type="text" size="128" value="[(M-H)]-,[M-H]-,[(M+Cl)]-,[M+Cl]-" help="">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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177 <sanitizer>
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178 <valid initial="string.printable">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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179 <remove value='"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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180 </valid>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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181 <mapping initial="none">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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182 <add source='"' target='\"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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183 </mapping>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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184 </sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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185 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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186
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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187 <!-- Positive precursors -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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188 <param name="pos" label="List of positive precursors" type="text" size="128" value="[(M+H)]+,[M+H]+,[(M+Na)]+,[M+Na]+,[(M+K)]+,[M+K]+" help="">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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189 <sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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190 <valid initial="string.printable">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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191 <remove value='"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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192 </valid>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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193 <mapping initial="none">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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194 <add source='"' target='\"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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195 </mapping>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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196 </sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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197 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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198 </when>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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199 </conditional>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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200
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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201 <!-- OUTPUT -->
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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202 <!-- Molecule IDs separator character -->
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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203 <param name="molidssep" label="Molecule IDs separator character" type="text" size="3" value="|" help="">
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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204 <sanitizer>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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205 <valid initial="string.printable">
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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206 <remove value='"'/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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207 </valid>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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208 <mapping initial="none">
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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209 <add source='"' target='\"'/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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210 </mapping>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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211 </sanitizer>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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212 </param>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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213
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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214 </inputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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215
6
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216 <!--=======
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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217 = OUTPUTS =
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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218 ========-->
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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219
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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220 <outputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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221
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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222 <!-- Output file -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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223 <data name="mainoutput" label="lcmsmatch_${mzrtinput.name}" format="tabular"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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224 <data name="peaksoutput" label="lcmsmatch_${mzrtinput.name}_peaks" format="tabular"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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225 <data name="htmloutput" label="lcmsmatch_${mzrtinput.name}.html" format="html"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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226
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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227 </outputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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228
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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229 <!--=====
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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230 = TESTS =
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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231 ======-->
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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232
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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233 <tests>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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234
1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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235 <!-- File database test -->
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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236 <test>
1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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237 <param name="dbtype" value="inhouse"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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238 <param name="dburl" value="filedb.tsv"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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239 <param name="dbfields" value=""/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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240 <param name="dbmsmodes" value=""/>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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241 <param name="mzrtinput" value="mz-input-small.tsv"/>
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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242 <param name="inputmzfield" value="mzmed"/>
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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243 <param name="inputrtfield" value="rtmed"/>
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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244 <param name="mzmode" value="pos"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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245 <output name="mainoutput" file="filedb-small-mz-match-output.tsv"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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246 <output name="peaksoutput" file="filedb-small-mz-match-peaks-output.tsv"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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247 <output name="htmloutput" file="filedb-small-mz-match-html-output.html"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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248 </test>
1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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249
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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250 <!-- File database test -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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251 <!--
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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252 <test>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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253 <param name="dbtype" value="peakforest"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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254 <param name="dbtoken" value="@PEAKFOREST_TOKEN@"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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255 <param name="mzrtinput" value="mz-input-small.tsv"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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256 <param name="inputfields" value=""/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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257 <param name="mzmode" value="pos"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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258 <output name="mainoutput">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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259 <assert_contents>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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260 <has_text text="mz"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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261 </assert_contents>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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262 </output>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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263 </test>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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264 -->
0
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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265 </tests>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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266
6
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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267 <!--====
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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268 = HELP =
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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269 =====-->
0
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270
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271 <help>
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272 <!-- @@@BEGIN_RST@@@ -->
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273
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274 ==============
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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275 LC/MS matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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276 ==============
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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277
1
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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278 This tool performs LC/MS matching on an input list of MZ/RT values, using either a provided in-house single file database or a connection to Peakforest database.
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279
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280 --------
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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281 Database
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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282 --------
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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283
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284 When selecting the database, you have the choice between a Peakforest database or an in-house file.
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285
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286 For the Peakforest database, a default REST web base address is already provided. But you can change it to use a custom database. A field is also available for setting a token key in case the access to the Peakforest database you want to use is restricted. This is the case of the default database URL.
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287
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288 For the in-house file, please refer to the paragraph "Single file database" below.
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289
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290 -----------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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291 Input files
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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292 -----------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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293
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294 Be careful to always provide UTF-8 encoded files, unless you do not use special characters at all. For instance, greek letters in molecule names give errors if the file is in latin1 (ISO 8859-1) or Windows 1252 (not distinguishable from latin1) encoding.
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295
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296 Single file database
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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297 ====================
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298
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299 The database used is provided as a single file, in tabular format, through the *Database file* field. This file must contain a list of MS peaks, with possibly retention times.
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300 Peaks are "duplicated" as much as necessary. For instance if 3 retention times are available on a compound with 10 peaks in positive mode, then there will be 30 lines for this compound in positive mode.
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301
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302 The file must contain a header with the column names. The names are free, but must be provided through the different fields named *Database file ... column name*.
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303 Then you must provide the values used to identify the MS modes (positive and negative).
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304
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305 A last information about the single file database is the unit of the retention times, either in seconds or in minutes.
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306
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307 Example of database file (totally fake, no meaning):
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308
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309 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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310 | molid | mode | mz | composition | attribution | col | rt | molcomp | molmass | molnames |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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311 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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312 | A10 | "POS" | 112.07569 | "P9Z6W410 O" | "[(M+H)-(H2O)-(NH3)]+" | "colzz" | 5.69 | "J114L6M62O2" | 146.10553 | "Blablaine'" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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313 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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314 | A10 | "POS" | 112.07569 | "P9Z6W410 O" | "[(M+H)-(H2O)-(NH3)]+" | "col12" | 0.8 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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315 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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316 | A10 | "POS" | 112.07569 | "P9Z6W410 O" | "[(M+H)-(H2O)-(NH3)]+" | "somecol" | 8.97 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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317 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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318 | A10 | "POS" | 191.076694 | "P92Z6W413 Na2 O2" | "[(M-H+2Na)]+" | "colAA" | 1.58 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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319 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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320 | A10 | "POS" | 191.076694 | "P92Z6W413 Na2 O2" | "[(M-H+2Na)]+" | "colzz2" | 4.08 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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321 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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322 | A10 | "POS" | 294.221687 | "U1113P94ZW429 O4" | "[(2M+H)]+ (13C)" | "somecol" | 8.97 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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323 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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324 | A10 | "POS" | 72.080775 | "P9Z4W410 O0" | "[(M+H)-(J15L2M6O2)]+" | "hcoltt" | 0.8 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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325 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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326 | A10 | "POS" | 112.07569 | "P9Z6W410 O" | "[(M+H)-(H2O)-(NH3)]+" | "colzz3" | 4.54 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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327 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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328 | A10 | "POS" | 72.080775 | "P9Z4W410 O0" | "[(M+H)-(J15L2M6O2)]+" | "colzz3" | 4.54 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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329 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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330 | A10 | "POS" | 72.080775 | "P9Z4W410 O0" | "[(M+H)-(J15L2M6O2)]+" | "colpp" | 0.89 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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331 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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332 | A10 | "POS" | 145.097154 | "P92Z6W413 O2" | "[(M+H)-(H2)]+" | "hcoltt" | 0.8 | "J114L6M62O2" | 146.10553 | "Blablaine" |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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333 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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334
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335 MZ/RT input file
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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336 ================
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337
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338 The input to provide is a file, in a tabular format (or TSV: Tab Seperated Values), containing the list of M/Z values, with possibly also RT values.
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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339
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340 The column names for the M/Z and RT values must be provided through the fields *Input file MZ column name* and *Input file RT column name*.
b8f70d8216b3 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
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341 As a consequence, the file must contain a header line.
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342
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343 The unit of the retention time has to be provided with the field *Retention time unit*.
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344
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345 Example of file input:
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346
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347 +-------------+-------------+
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348 | mz | rt |
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349 +-------------+-------------+
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350 | 75.02080998 | 49.38210915 |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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351 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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352 | 75.05547146 | 0.658528069 |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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353 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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354 | 75.08059797 | 1743.94267 |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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355 +-------------+-------------+
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356 | 76.03942694 | 51.23158899 |
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357 +-------------+-------------+
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358 | 76.07584477 | 50.51249853 |
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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359 +-------------+-------------+
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360 | 76.07593168 | 0.149308136 |
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361 +-------------+-------------+
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362
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363 ------------
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364 M/Z matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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365 ------------
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366
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367 In the simplest form of the algorithm only the *m/z* values are matched against the database peaks. This happens if both *Retention time match* and *Precursor match* are off.
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368
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369 The first parameter is the MS mode, specified through the *MS mode* parameter.
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370
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371 The parameters *M/Z precision* and *M/Z shift* are used by the algorithm in the following formula in order to match an *m/z* value:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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372
6
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373 mz (1 + (- shift - precision) / 10^6) &lt; mzref &lt; mz (1 + (- shift - precision) / 10^6)
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374
6
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375 Where *mzref* is the M/Z of reference from the database peak that is tested. If this double inequality is true, then the *m/z* value is matched with this peak.
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376
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377 --------------------
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378 Retention time match
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379 --------------------
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380
6
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381 If at least one column is selected inside the *Chromatographic columns* parameter section, then retention time is also matched, in addition to the *m/z* value, according to the following formula:
0
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382
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383 rt - x - rt^y &lt; colrt &lt; rt + x + rt^y
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384
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385 Where *x* is the value of the parameter *RTX* and *y* the value of the parameter *RTY*.
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386
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387 If for a reference compound the database does not contain retention time for at least one of the specified columns, then only the *m/z* value is matched against the peaks of the reference compound. This means that in the results you can find compounds that do no match the provided retention time value.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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388
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389 The *RTZ* parameter is used in the *Precursor match* algorithm (see below).
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390
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391 ---------------
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392 Precursor match
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393 ---------------
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394
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395 If the "Precursor match" option is enabled inside the parameters section, then a more sophisticated version of the algorithm, which is executed in two steps, is used.
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396
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397 This algorithm takes two more parameters, one for each MS mode. These are the lists of precursors. Since the matching is run for one MS mode only, only one of the two parameters is used. Inside the single file database, all the peaks whose **attr** column value is equal to one of the precursor listed in *List of negative precursors* or *List of positive precursors*, depending on the mode, are considered as precursor peaks.
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398
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399 M/Z matching using precursor matching
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400 =====================================
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401
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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402 1. Using the normal M/Z matching algorithm described above, we first look only for precursor peaks ([(M+H)]+, [(M+Na)]+, [(M+Cl)]-, ...).
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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403 2. From step 1, we construct a list of matched molecules.
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404 3. We look at all peaks inside the molecule list obtained in step 2, using the normal M/Z matching algorithm described above.
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405
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406 MZ/RT matching using precursor matching
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407 =======================================
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408
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409 1. Using the normal MZ/RT matching algorithm described above, we first look only for precursor peaks ([(M+H)]+, [(M+Na)]+, [(M+Cl)]-, ...).
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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410 2. From step 1, we construct a list of matched molecules, retaining the matched retention time of each molecule.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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411 3. For each input couple (m/z,rt), we look at all peaks inside the molecules taken from step 2, whose matched retention time between *rt - z* and *rt + z*, where *z* is the value of parameter *RTZ*.
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412
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413 ---------------
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414 Output settings
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415 ---------------
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416
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417 The *Molecule IDs separator character* is used to customize the character used to separate the molecule IDs of the **molid** column inside the *main* output file.
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418
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419 Output files
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420 ============
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421
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422 Three files are output by the tool.
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423
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424 +-------------+--------------------------------------+--------------------------------------------------------+
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425 | Outputs | File name | Description |
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426 +-------------+--------------------------------------+--------------------------------------------------------+
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427 | Main output | lcmsmatching_{input_file_name} | Contains the list of compounds that have been matched. |
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428 +-------------+--------------------------------------+--------------------------------------------------------+
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429 | Peak list | lcmsmatching_peaks_{input_file_name} | Contains all matched database peaks. |
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430 +-------------+--------------------------------------+--------------------------------------------------------+
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431 | HTML output | lcmsmatching_{input_file_name}.html | Contains the two tables on one page. |
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432 +-------------+--------------------------------------+--------------------------------------------------------+
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433
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434 The **main** output is identical to the input file, to which is added an *msmatching* column. This column contains a list of IDs of the compounds that have been matched for this couple of (m/z, rt) values.
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435
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436 The **peak list** output contains all database peaks that have been matched, for each (m/z, rt) input couple. Thus for each (m/z, rt) couple, there will be zero, one or more matched peaks output. The columns output are *mz*, *rt*, *id*, *mztheo*, *col*, *colrt*, *attribution* and *composition*, where *id* is the compound ID, *mztheo* is the theoretical mass of the fragment, *col* is the matched column and *colrt* is the retention time measured on the column for the reference compound.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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437
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438 The **HTML** output contains the peak table with links toward HMDB, KEGG, ChEBI and PubChem public databases, when IDs are available.
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439
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440 =====
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441 About
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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442 =====
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443
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444 .. class:: infomark
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445
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446 **Author**
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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447 Pierrick Roger (pierrick.roger@cea.fr) wrote this MS matching method.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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448 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en).
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449
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450 .. class:: infomark
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451
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452 **Acknowledgement**
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453 Data and algorithms have been kindly provided by Christophe Junot at *DSV/IBITEC-S/SPI* (*CEA/Saclay*), from a former application developped by Cyrille Petat and Arnaud Martel at *DSV/IBITEC-S/DIR* (*CEA/Saclay*).
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454
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455 .. class:: infomark
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456
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457 **Please cite**
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458 R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
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459
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460 <!-- @@@END_RST@@@ -->
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461 </help>
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462
6
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463 <!--=========
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464 = CITATIONS =
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465 ==========-->
0
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466
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467 <citations/>
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468
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469 </tool>