lcmsmatching: lcmsmatching.xml annotate

annotate lcmsmatching.xml @ 5:18254e8d1b72 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty

author	prog
date	Thu, 16 Mar 2017 08:15:11 -0400
parents	1ba222315fd5
children	b8f70d8216b3

rev	line source
5 18254e8d1b72 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty prog parents: 4 diff changeset	1 <tool id="lcmsmatching" name="LC/MS matching" version="3.2.2" profile="16.01">
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	2
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	3 <description>Annotation of MS peaks using matching on a spectra database.</description>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	4
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	5 <requirements>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	6 <requirement type="package" version="1.20.0">r-getopt</requirement>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	7 <requirement type="package" version="1.0.0">r-stringr</requirement>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	8 <requirement type="package" version="1.8.3">r-plyr</requirement>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	9 <requirement type="package" version="3.98">r-xml</requirement>
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	10 <requirement type="package" version="1.0_6">r-bitops</requirement>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	11 <requirement type="package" version="1.95">r-rcurl</requirement>
4 1ba222315fd5 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb prog parents: 3 diff changeset	12 <requirement type="package" version="1.3">r-jsonlite</requirement>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	13 </requirements>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	14
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	15 <code file="list-chrom-cols.py"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	16
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	17 <!--~~~~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	18 ~ COMMAND ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	19 ~~~~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	20
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	21 <command>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	22 <![CDATA[
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	23 ## @@@BEGIN_CHEETAH@@@
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	24 $__tool_directory__/search-mz -i "$mzrtinput"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	25
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	26 ## Database
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	27 #if $db.dbtype == "inhouse"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	28 -d file
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	29 --db-fields "$db.dbfields"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	30 --db-ms-modes "$db.dbmsmodes"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	31 #end if
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	32 #if $db.dbtype == "peakforest"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	33 -d peakforest
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	34 --db-token "$db.dbtoken"
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	35 #end if
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	36 --url "$db.dburl"
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	37
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	38 ## M/Z matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	39 -m $mzmode -p $mzprec -s $mzshift
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	40
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	41 ## Precursor matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	42 #if $prec.match == "true"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	43 --precursor-match --pos-prec "$prec.pos" --neg-prec "$prec.neg"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	44 #end if
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	45 #if $prec.match == "true" and $chromcols:
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	46 --precursor-rt-tol $tolz
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	47 #end if
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	48
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	49 ## Chromatographic columns options and retention matching
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	50 #if $chromcols:
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	51 -c "$chromcols" --check-cols --rttolx $tolx --rttoly $toly
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	52 #end if
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	53
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	54 ## Table outputs
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	55 -o "$mainoutput" --peak-output-file "$peaksoutput" --same-rows --same-cols
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	56
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	57 ## HTML output
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	58 --html-output-file "$htmloutput" --no-main-table-in-html-output
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	59
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	60 ## Fields of input file
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	61 --input-col-names "$inputfields"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	62
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	63 ## Ouput setting
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	64 #if $out.enabled == "true"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	65 --output-col-names "$out.outputfields"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	66 --molids-sep "$out.molidssep"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	67 #else
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	68 --molids-sep "\|"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	69 #end if
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	70 ## @@@END_CHEETAH@@@
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	71 ]]></command>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	72
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	73 <!--~~~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	74 ~ INPUTS ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	75 ~~~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	76
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	77 <inputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	78
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	79 <!-- DATABASE -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	80
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	81 <conditional name="db">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	82
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	83 <param name="dbtype" label="Database" type="select" refresh_on_change="true">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	84 <option value="inhouse">In-house</option>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	85 <option value="peakforest">Peakforest</option>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	86 </param>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	87
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	88 <when value="inhouse">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	89 <!-- Database file -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	90 <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 prog parents: 0 diff changeset	91
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	92 <!-- File database field names -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	93 <param name="dbfields" label="File database column names" type="text" size="256" value="mztheo=mztheo,chromcolrt=chromcolrt,compoundid=compoundid,chromcol=chromcol,msmode=msmode,peakattr=peakattr,peakcomp=peakcomp,fullnames=fullnames,compoundmass=compoundmass,compoundcomp=compoundcomp,inchi=inchi,inchikey=inchikey,pubchemcompid=pubchemcompid,chebiid=chebiid,hmdbid=hmdbid,keggid=keggid" refresh_on_change="true" help=""/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	94
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	95 <!-- File database MS modes -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	96 <param name="dbmsmodes" label="File database MS modes" type="text" size="32" value="pos=POS,neg=NEG" help=""/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	97
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	98 <param name="dbtoken" type="text" size="32" value="" hidden="true"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	99 </when>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	100
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	101 <when value="peakforest">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	102 <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 prog parents: 0 diff changeset	103
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	104 <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 prog parents: 0 diff changeset	105
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	106 <param name="dbfields" type="text" size="32" value="" hidden="true"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	107 </when>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	108 </conditional>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	109
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	110 <!-- INPUT -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	111
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	112 <!-- Input file -->
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	113 <param name="mzrtinput" label="Input file - MZ(/RT) values" type="data" format="tabular,tsv" help="Decimal: '.', missing: NA, mode: character and numerical, sep: tabular. RT values must be in seconds."/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	114
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	115 <!-- Input field names -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	116 <param name="inputfields" label="Input file column names" type="text" size="32" value="mz=mzmed,rt=rtmed" help=""/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	117
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	118 <!-- M/Z MATCHING -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	119
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	120 <!-- Mode -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	121 <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 prog parents: 0 diff changeset	122 <option value="pos">Positive</option>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	123 <option value="neg">Negative</option>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	124 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	125
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	126 <!-- MZ matching parameters -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	127 <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 prog parents: 0 diff changeset	128 <param name="mzshift" label="M/Z shift (in ppm)" type="float" help="" value="0"/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	129
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	130 <!-- RETENTION TIME PARAMETERS -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	131
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	132 <!-- List of chromatographic columns -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	133 <param name="chromcols" type="select" label="Chromatographic columns" multiple="true" dynamic_options="get_chrom_cols(dbtype = db['dbtype'], dburl = db['dburl'], dbtoken = db['dbtoken'], dbfields = db['dbfields'])" 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 prog parents: diff changeset	134
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	135 <!-- Tolerances -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	136 <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 prog parents: 0 diff changeset	137 <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 prog parents: 0 diff changeset	138 <param name="tolz" label="RTZ retention time tolerance, used when precursor matching is enabled." type="float" help="" value="5"/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	139
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	140 <!-- PRECURSOR MATCH -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	141 <conditional name="prec">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	142
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	143 <param name="match" label="Precursor match" type="select">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	144 <option value="false">Off</option>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	145 <option value="true">On</option>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	146 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	147
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	148 <when value="false"></when>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	149 <when value="true">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	150 <!-- Negative precursors -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	151 <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 prog parents: diff changeset	152 <sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	153 <valid initial="string.printable">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	154 <remove value='"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	155 </valid>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	156 <mapping initial="none">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	157 <add source='"' target='\"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	158 </mapping>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	159 </sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	160 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	161
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	162 <!-- Positive precursors -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	163 <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 prog parents: diff changeset	164 <sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	165 <valid initial="string.printable">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	166 <remove value='"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	167 </valid>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	168 <mapping initial="none">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	169 <add source='"' target='\"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	170 </mapping>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	171 </sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	172 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	173 </when>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	174 </conditional>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	175
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	176 <!-- OUTPUT -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	177 <conditional name="out">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	178
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	179 <param name="enabled" label="Output settings" type="select">
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	180 <option value="false">Default</option>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	181 <option value="true">Customized</option>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	182 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	183
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	184 <when value="false"></when>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	185 <when value="true">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	186
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	187 <!-- Output field names -->
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	188 <param name="outputfields" label="Output column names" type="text" size="256" value="mz=mz,rt=rt,chromcol=chromcol,chromcolrt=chromcolrt,compoundid=compoundid,peakattr=peakattr,peakcomp=peakcomp,intensity=intensity,relative.intensity=relative.intensity,mzexp=mzexp,mztheo=mztheo,fullnames=fullnames,compoundmass=compoundmass,compoundcomp=compoundcomp,inchi=inchi,inchikey=inchikey,pubchemcompid=pubchemcompid,chebiid=chebiid,hmdbid=hmdbid,keggid=keggid" help=""/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	189
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	190 <!-- Molecule IDs separator character -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	191 <param name="molidssep" label="Molecule IDs separator character" type="text" size="3" value="\|" help="">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	192 <sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	193 <valid initial="string.printable">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	194 <remove value='"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	195 </valid>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	196 <mapping initial="none">
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	197 <add source='"' target='\"'/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	198 </mapping>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	199 </sanitizer>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	200 </param>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	201 </when>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	202 </conditional>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	203
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	204 </inputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	205
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	206 <!--~~~~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	207 ~ OUTPUTS ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	208 ~~~~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	209
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	210 <outputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	211
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	212 <!-- Output file -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	213 <data name="mainoutput" label="lcmsmatch_${mzrtinput.name}" format="tabular"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	214 <data name="peaksoutput" label="lcmsmatch_${mzrtinput.name}_peaks" format="tabular"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	215 <data name="htmloutput" label="lcmsmatch_${mzrtinput.name}.html" format="html"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	216
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	217 </outputs>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	218
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	219 <!--~~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	220 ~ TESTS ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	221 ~~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	222
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	223 <tests>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	224
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	225 <!-- File database test -->
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	226 <test>
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	227 <param name="dbtype" value="inhouse"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	228 <param name="dburl" value="filedb.tsv"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	229 <param name="dbfields" value=""/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	230 <param name="dbmsmodes" value=""/>
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	231 <param name="mzrtinput" value="mz-input-small.tsv"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	232 <param name="inputfields" value=""/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	233 <param name="mzmode" value="pos"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	234 <output name="mainoutput" file="filedb-small-mz-match-output.tsv"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	235 <output name="peaksoutput" file="filedb-small-mz-match-peaks-output.tsv"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	236 <output name="htmloutput" file="filedb-small-mz-match-html-output.html"/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	237 </test>
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	238
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	239 <!-- File database test -->
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	240 <!--
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	241 <test>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	242 <param name="dbtype" value="peakforest"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	243 <param name="dbtoken" value="@PEAKFOREST_TOKEN@"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	244 <param name="mzrtinput" value="mz-input-small.tsv"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	245 <param name="inputfields" value=""/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	246 <param name="mzmode" value="pos"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	247 <output name="mainoutput">
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	248 <assert_contents>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	249 <has_text text="mz"/>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	250 </assert_contents>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	251 </output>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	252 </test>
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	253 -->
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	254 </tests>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	255
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	256 <!--~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	257 ~ HELP ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	258 ~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	259
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	260 <help>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	261 <!-- @@@BEGIN_RST@@@ -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	262
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	263 ==============
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	264 LC/MS matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	265 ==============
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	266
1 45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	267 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.
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	268
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	269 --------
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	270 Database
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	271 --------
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	272
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	273 When selecting the database, you have the choice between a Peakforest database or an in-house file.
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	274
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	275 For the Peakforest database, a default REST web base address is already provided. But you can change it of you want 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.
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	276
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty prog parents: 0 diff changeset	277 For the in-house file, please refer to the paragraph "Single file database" below.
0 3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	278
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	279 -----------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	280 Input files
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	281 -----------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	282
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	283 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	284
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	285 Single file database
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	286 ====================
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	287
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	288 The database used is provided as a single file, in tabular format, through the Database file field. This file contains a list of MS peaks, with retention times.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	289 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 compounds in positive mode.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	290
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	291 The file must contain a header with the column names. The names are free, but must be provided through the File database column names field.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	292 In this field, each column is identified with a tag, and the columns names are listed as a comma separated list of tag/name couples (separated by character `=`). The allowed tags are the following ones:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	293
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	294 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	295 \| Column tag \| Compulsory \| Values \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	296 +==============+============+============================================================================================================+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	297 \| mztheo \| Yes \| The m/z values. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	298 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	299 \| mode \| Yes \| The MS mode. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	300 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	301 \| molid \| Yes \| This is the identifier of your compound. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	302 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	303 \| colrt \| No \| The retention time values in seconds. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	304 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	305 \| col \| No \| The chromatographic column associated with the retention time. Compulsory if retention times are provided. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	306 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	307 \| attr \| No \| The attribution of the peak (e.g.: ``[(M+H)-(H2O)-(NH3)]+``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	308 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	309 \| comp \| No \| The composition of the peak (e.g.: ``C6 H10 N O``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	310 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	311 \| molcomp \| No \| The composition of the molecule. (e.g.: ``C6H14N2O2``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	312 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	313 \| molmass \| No \| The mass of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	314 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	315 \| molnames \| No \| The names of the molecule, as a semicolon separated list. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	316 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	317 \| inchi \| No \| The InChI of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	318 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	319 \| inchikey \| No \| The InChI key of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	320 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	321 \| pubchem \| No \| The PubChem ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	322 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	323 \| chebi \| No \| The ChEBI ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	324 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	325 \| hmdb \| No \| The HMDB ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	326 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	327 \| kegg \| No \| The KEGG ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	328 +--------------+------------+------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	329
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	330 The field File database MS modes allows you to personalize the MS mode identifiers. The value of the field is a comma separated list of mode/name couples (separated by character `=`)..
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	331 For instance, if in your database file you use characters '+' and '-' to identify the modes, then you must set the field to `pos=+,neg=-`.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	332
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	333 Example of database file (totally fake, no meaning):
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	334
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	335 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	336 \| molid \| mode \| mz \| composition \| attribution \| col \| rt \| molcomp \| molmass \| molnames \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	337 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	338 \| 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 prog parents: diff changeset	339 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	340 \| 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 prog parents: diff changeset	341 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	342 \| 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 prog parents: diff changeset	343 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	344 \| 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 prog parents: diff changeset	345 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	346 \| 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 prog parents: diff changeset	347 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	348 \| 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 prog parents: diff changeset	349 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	350 \| 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 prog parents: diff changeset	351 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	352 \| 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 prog parents: diff changeset	353 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	354 \| 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 prog parents: diff changeset	355 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	356 \| 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 prog parents: diff changeset	357 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	358 \| 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 prog parents: diff changeset	359 +-------+-------+------------+--------------------+-------------------------+-----------+-------+---------------+-----------+--------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	360
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	361 MZ/RT input file
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	362 ================
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	363
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	364 The input to provide is a file, in a tabular format (or TSV: Tab Seperated Values), containing the list of MZ/RT values.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	365
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	366 The following columns will be used:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	367
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	368 +--------------+------------+---------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	369 \| Column tag \| Compulsory \| Values \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	370 +==============+============+=======================================+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	371 \| mz \| Yes \| The m/z values. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	372 +--------------+------------+---------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	373 \| rt \| No \| The retention time values in seconds. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	374 +--------------+------------+---------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	375
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	376 The file may contain a header line, in which case you have to provide the column names through the Input file column names field, which consists in a comma separated list of tag/name couples (separated by character `=`). If your file does not contain a header line, then you must provide the column numbers. Examples:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	377
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	378 * With a header line having name MASS for mz column and RET for rt column: `mz=MASS,rt=RET`.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	379 * With no header line: `mz=1,rt=2`.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	380
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	381 Since the MS spectrum mode can not be known from the file, an MS mode radio button field is provided for setting the mode.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	382
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	383 Example of file input:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	384
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	385 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	386 \| mz \| rt \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	387 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	388 \| 75.02080998 \| 49.38210915 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	389 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	390 \| 75.05547146 \| 0.658528069 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	391 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	392 \| 75.08059797 \| 1743.94267 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	393 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	394 \| 76.03942694 \| 51.23158899 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	395 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	396 \| 76.07584477 \| 50.51249853 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	397 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	398 \| 76.07593168 \| 0.149308136 \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	399 +-------------+-------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	400
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	401 ------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	402 M/Z matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	403 ------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	404
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	405 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	406
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	407 The first parameter is the MS mode, specified through the MS mode parameter.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	408
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	409 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 prog parents: diff changeset	410
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	411 mz (1 + (- shift - precision) / 10^6) < mztheo < mz (1 + (- shift - precision) / 10^6)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	412
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	413 Where mztheo is the theoretical mass of the database peak that is tested. If this double inequality is true, then the m/z value is matched with this peak.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	414
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	415 --------------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	416 Retention time match
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	417 --------------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	418
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	419 If at least one column is checked inside the Columns parameter section, then retention time is also matched, in addition to the m/z value, according to the following formula:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	420
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	421 rt - x - rt^y < colrt < rt + x + rt^y
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	422
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	423 Where x is the value of the parameter RTX and y the value of the parameter RTY.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	424
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	425 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 prog parents: diff changeset	426
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	427 The RTZ parameter is used in the Precursor match algorithm (see below).
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	428
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	429 ---------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	430 Precursor match
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	431 ---------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	432
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	433 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	434
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	435 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	436
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	437 M/Z matching using precursor matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	438 =====================================
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	439
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	440 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 prog parents: diff changeset	441 2. From step 1, we construct a list of matched molecules.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	442 3. We look at all peaks inside the molecule list obtained in step 2, using the normal M/Z matching algorithm described above.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	443
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	444 MZ/RT matching using precursor matching
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	445 =======================================
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	446
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	447 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 prog parents: diff changeset	448 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 prog parents: diff changeset	449 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	450
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	451 ---------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	452 Output settings
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	453 ---------------
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	454
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	455 The Output column names parameter is used to customize the columns of the output files. As with the File database column names parameter, each column is identified with a tag, and the columns names are listed as a comma separated list of tag/name couples (separated by character `=`). The allowed tags are the following ones:
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	456
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	457 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	458 \| Column tag \| Values \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	459 +==============+=================================================================================================================================+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	460 \| mz \| The m/z values from the input file. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	461 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	462 \| mztheo \| The m/z values from the database. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	463 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	464 \| molid \| This is the identifier of your compound. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	465 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	466 \| rt \| The retention time values in seconds from the input file. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	467 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	468 \| col \| The chromatographic column associated with the retention time. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	469 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	470 \| colrt \| The retention time associated with the matched chromatographic column. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	471 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	472 \| msmatching \| The list IDs of matched molecules. IDs are separated by the character specified in the Molecule IDs separator character field \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	473 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	474 \| attr \| The attribution of the peak (e.g.: ``[(M+H)-(H2O)-(NH3)]+``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	475 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	476 \| comp \| The composition of the peak (e.g.: ``C6 H10 N O``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	477 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	478 \| molcomp \| The composition of the molecule. (e.g.: ``C6H14N2O2``). \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	479 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	480 \| molmass \| The mass of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	481 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	482 \| molnames \| The names of the molecule, as a semicolon separated list. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	483 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	484 \| inchi \| The InChI of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	485 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	486 \| inchikey \| The InChI key of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	487 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	488 \| pubchem \| The PubChem ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	489 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	490 \| chebi \| The ChEBI ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	491 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	492 \| hmdb \| The HMDB ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	493 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	494 \| kegg \| The KEGG ID of the molecule. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	495 +--------------+---------------------------------------------------------------------------------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	496
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	497 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	498
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	499 Output files
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	500 ============
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	501
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	502 Three files are output by the tool.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	503
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	504 +-------------+--------------------------------------+--------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	505 \| Outputs \| File name \| Description \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	506 +-------------+--------------------------------------+--------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	507 \| Main output \| lcmsmatching_{input_file_name} \| Contains the list of compounds that have been matched. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	508 +-------------+--------------------------------------+--------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	509 \| Peak list \| lcmsmatching_peaks_{input_file_name} \| Contains all matched database peaks. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	510 +-------------+--------------------------------------+--------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	511 \| HTML output \| lcmsmatching_{input_file_name}.html \| Contains the two tables on one page. \|
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	512 +-------------+--------------------------------------+--------------------------------------------------------+
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	513
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	514 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.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	515
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	516 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 prog parents: diff changeset	517
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	518 The HTML output contains the peak table with links toward HMDB, KEGG, ChEBI and PubChem public databases, when IDs are available.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	519
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	520 =====
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	521 About
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	522 =====
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	523
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	524 .. class:: infomark
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	525
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	526 Author
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	527 Pierrick Roger (pierrick.roger@cea.fr) wrote this MS matching method.
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	528 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en).
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	529
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	530 .. class:: infomark
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	531
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	532 Acknowledgement
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	533 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).
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	534
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	535 .. class:: infomark
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	536
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	537 Please cite
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	538 R Core Team (2013). R: A language and Environment for Statistical Computing. http://www.r-project.org
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	539
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	540 <!-- @@@END_RST@@@ -->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	541 </help>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	542
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	543 <!--~~~~~~~~~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	544 ~ CITATIONS ~
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	545 ~~~~~~~~~~-->
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	546
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	547 <citations/>
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	548
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f prog parents: diff changeset	549 </tool>

Mercurial > repos > prog > lcmsmatching

annotate lcmsmatching.xml @ 5:18254e8d1b72 draft