Mercurial > repos > prog > lcmsmatching
comparison lcmsmatching.xml @ 2:20d69a062da3 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
| author | prog |
|---|---|
| date | Thu, 02 Mar 2017 08:55:00 -0500 |
| parents | 253d531a0193 |
| children | f61ce21ed17c |
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| 1:253d531a0193 | 2:20d69a062da3 |
|---|---|
| 1 <tool id="lcmsmatching" name="LC/MS matching" version="3.0"> | 1 <tool id="lcmsmatching" name="LC/MS matching" version="3.1.7" profile="16.01"> |
| 2 | 2 |
| 3 <description>Annotation of MS peaks using matching on a spectra database.</description> | 3 <description>Annotation of MS peaks using matching on a spectra database.</description> |
| 4 | 4 |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="3.2.2">R</requirement> | 6 <requirement type="package" version="3.2.2">R</requirement> |
| 89 <when value="inhouse"> | 89 <when value="inhouse"> |
| 90 <!-- Database file --> | 90 <!-- Database file --> |
| 91 <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."/> | 91 <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."/> |
| 92 | 92 |
| 93 <!-- File database field names --> | 93 <!-- File database field names --> |
| 94 <param name="dbfields" label="File database column names" type="text" size="256" value="mztheo=mztheo,colrt=colrt,molid=molid,col=col,mode=mode,attr=attr,comp=comp,molnames=molnames,molcomp=molcomp,molmass=molmass,inchi=inchi,inchikey=inchikey,pubchem=pubchem,chebi=chebi,hmdb=hmdb,kegg=kegg" refresh_on_change="true" help=""/> | 94 <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=""/> |
| 95 | 95 |
| 96 <!-- File database MS modes --> | 96 <!-- File database MS modes --> |
| 97 <param name="dbmsmodes" label="File database MS modes" type="text" size="32" value="pos=POS,neg=NEG" help=""/> | 97 <param name="dbmsmodes" label="File database MS modes" type="text" size="32" value="pos=POS,neg=NEG" help=""/> |
| 98 | 98 |
| 99 <param name="dbtoken" type="text" size="32" value="" hidden="true"/> | 99 <param name="dbtoken" type="text" size="32" value="" hidden="true"/> |
| 176 | 176 |
| 177 <!-- OUTPUT --> | 177 <!-- OUTPUT --> |
| 178 <conditional name="out"> | 178 <conditional name="out"> |
| 179 | 179 |
| 180 <param name="enabled" label="Output settings" type="select"> | 180 <param name="enabled" label="Output settings" type="select"> |
| 181 <option value="false">Off</option> | 181 <option value="false">Default</option> |
| 182 <option value="true">On</option> | 182 <option value="true">Customized</option> |
| 183 </param> | 183 </param> |
| 184 | 184 |
| 185 <when value="false"></when> | 185 <when value="false"></when> |
| 186 <when value="true"> | 186 <when value="true"> |
| 187 | 187 |
| 188 <!-- Output field names --> | 188 <!-- Output field names --> |
| 189 <param name="outputfields" label="Output column names" type="text" size="256" value="mz=mz,rt=rt,col=col,colrt=colrt,molid=molid,attr=attr,comp=comp,int=int,rel=rel,mzexp=mzexp,mztheo=mztheo,molnames=molnames,molcomp=molcomp,molmass=molmass,inchi=inchi,inchikey=inchikey,pubchem=pubchem,chebi=chebi,hmdb=hmdb,kegg=kegg" help=""/> | 189 <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=""/> |
| 190 | 190 |
| 191 <!-- Molecule IDs separator character --> | 191 <!-- Molecule IDs separator character --> |
| 192 <param name="molidssep" label="Molecule IDs separator character" type="text" size="3" value="|" help=""> | 192 <param name="molidssep" label="Molecule IDs separator character" type="text" size="3" value="|" help=""> |
| 193 <sanitizer> | 193 <sanitizer> |
| 194 <valid initial="string.printable"> | 194 <valid initial="string.printable"> |