diff lcmsmatching.xml @ 2:20d69a062da3 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8

--- a/lcmsmatching.xml	Sat Sep 03 17:02:01 2016 -0400
+++ b/lcmsmatching.xml	Thu Mar 02 08:55:00 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="lcmsmatching" name="LC/MS matching" version="3.0">
+<tool id="lcmsmatching" name="LC/MS matching" version="3.1.7" profile="16.01">
 
 	<description>Annotation of MS peaks using matching on a spectra database.</description>
 
@@ -91,7 +91,7 @@
 				<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."/>
 
 				<!-- File database field names -->
-				<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=""/>
+				<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=""/>
 
 				<!-- File database MS modes -->
 				<param name="dbmsmodes" label="File database MS modes" type="text" size="32" value="pos=POS,neg=NEG" help=""/>
@@ -178,15 +178,15 @@
 		<conditional name="out">
 
 			<param name="enabled" label="Output settings" type="select">
-				<option value="false">Off</option>
-				<option value="true">On</option>
+				<option value="false">Default</option>
+				<option value="true">Customized</option>
 			</param>
 
 			<when value="false"></when>
 			<when value="true">
 
 				<!-- Output field names -->
-				<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=""/>
+				<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=""/>
 
 				<!-- Molecule IDs separator character -->
 				<param name="molidssep" label="Molecule IDs separator character" type="text" size="3" value="|" help="">