correction big dans mcq.read.metadata.template + MaJ de l'aide mcq.read.metadata.template.Rd

MCQR/R/mcq_write_metadata_template.R

@@ -39,6 +39,6 @@ mcq.write.metadata.template = function(object, file="metadata_template.tsv", fra
 	} else {
 		stop(paste("the class \"", class(object),"\" is not taken into account by mcq.write.metadata.template",sep=""))
 	}
-	mcq.write(metadata, type='ods', file)
+	mcq.write(metadata, type='ods', file=file)
   #priv.write.data(metadata, paste0(file,".ods"))
 }

MCQR/man/mcq.write.metadata.template.Rd

@@ -4,18 +4,18 @@
 
 \title{Export Metadata Template}
 
-\description{This function exports a template file allowing the user to describe the metadata, i.e. all the information regarding the injections.}
+\description{This function exports an ods file allowing the user to describe the metadata, i.e. all the information regarding the injections.}
 
-\usage{mcq.write.metadata.template(object, file="metadata_template.tsv", fractionation=FALSE)}
+\usage{mcq.write.metadata.template(object, file="metadata_template", fractionation=FALSE)}
 
 \arguments{
   \item{object}{an object of class 'cmcq.pepq.masschroq' or 'cmcq.pepq.masschroq.labeling' or 'cmcq.protq.spectralcounting'.}
-  \item{file}{a character string indicating the name of the file to export. By default, "metadata_template.tsv".}
+  \item{file}{a character string indicating the name of the file to export. By default, "metadata_template". Do not indicate an extention, it is automatically added.}
   \item{fractionation}{a boolean indicating whether the proteomics experiment includes fractionation.}
 }
 
 
-\value{When fractionation=FALSE, 'mcq.write.metadata.template' produces a tabulated text file containing two colums, "msrun" and "msrunfile", that are automatically filled in. When fractionation=TRUE, columns that describe fractions and tracks are automatically added. The user can open this file as a spreadsheet (for instance with LibreOffice Calc), complete empty columns and add as many columns as desired to describe injections. Once modified, the file must be saved in an ods format so that it can then be used as input in 'mcq.read.metadata'.}
+\value{When fractionation=FALSE, 'mcq.write.metadata.template' produces an ods file containing two colums, "msrun" and "msrunfile", that are automatically filled in. When fractionation=TRUE, columns that describe fractions and tracks are automatically added. The user can open this file as a spreadsheet (for instance with LibreOffice Calc), complete empty columns and add as many columns as desired to describe injections. Once modified, the file must be saved in the same ods format so that it can then be used as input in 'mcq.read.metadata'.}
 
 
 \author{PAPPSO (pappso-projetsbioinfo@groupes.renater.fr)}

new_example_data/script/lanceur_shotgun_strepto.R

@@ -29,6 +29,7 @@
 	my_peptide_file = "./output/XIC_result_pep_all.tsv"
 
 	raw_xic <- mcq.read.masschroq(protFile=my_protein_file, pepFile=my_peptide_file)
+	mcq.write.metadata.template(raw_xic, file="/home/blein/Bureau/Meli/Documents/mcqr/new_example_data/output/test_export_metadata")
 	my_metadata = mcq.read.metadata("./output/metadata_strepto.ods") 
 	raw_xic <- mcq.add.metadata(raw_xic, metadata=my_metadata)