# HG changeset patch
# User lecorguille
# Date 1541795190 18000
# Node ID 7b77a7238777b340c081944736697ea0f7be1116
# Parent  9128f47ffd12cde0df08aa7775d0d16f24f11462
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989

diff -r 9128f47ffd12 -r 7b77a7238777 lib.r
--- a/lib.r	Thu Oct 04 09:48:26 2018 -0400
+++ b/lib.r	Fri Nov 09 15:26:30 2018 -0500
@@ -198,6 +198,9 @@
     variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
     dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
 
+    # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
+    variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
+
     write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
     write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
 
@@ -260,9 +263,9 @@
     #Create the sampleMetada dataframe
     sampleMetadata <- xdata@phenoData@data
     rownames(sampleMetadata) <- NULL
-    colnames(sampleMetadata) <-  c("sampleMetadata", "class")
+    colnames(sampleMetadata) <-  c("sample_name", "class")
 
-    sampleNamesOrigin <- sampleMetadata$sampleMetadata
+    sampleNamesOrigin <- sampleMetadata$sample_name
     sampleNamesMakeNames <- make.names(sampleNamesOrigin)
 
     if (any(duplicated(sampleNamesMakeNames))) {
@@ -280,7 +283,7 @@
         }
     }
 
-    sampleMetadata$sampleMetadata <- sampleNamesMakeNames
+    sampleMetadata$sample_name <- sampleNamesMakeNames
 
 
     #For each sample file, the following actions are done
diff -r 9128f47ffd12 -r 7b77a7238777 macros_xcms.xml
--- a/macros_xcms.xml	Thu Oct 04 09:48:26 2018 -0400
+++ b/macros_xcms.xml	Fri Nov 09 15:26:30 2018 -0500
@@ -90,9 +90,6 @@
     </token>
 
     <xml name="input_peaklist">
-        <conditional name="peaklist">
-            <param name="peaklistBool" type="boolean" label="Get a Peak List" />
-            <when value="true">
               <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
               <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
               <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
@@ -102,6 +99,20 @@
                   <option value="intb">intb</option>
               </param>
               <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
+    </xml>
+
+    <xml name="input_peaklist_section">
+        <section name="peaklist" title="Peak List" expanded="True">
+            <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
+            <expand macro="input_peaklist"/>
+        </section>
+    </xml>
+
+    <xml name="input_peaklist_conditional">
+        <conditional name="peaklist">
+            <param name="peaklistBool" type="boolean" label="Get the Peak List" />
+            <when value="true">
+              <expand macro="input_peaklist"/>
             </when>
             <when value="false" />
         </conditional>
diff -r 9128f47ffd12 -r 7b77a7238777 test-data/noclass.merged.sampleMetadata.tsv
--- a/test-data/noclass.merged.sampleMetadata.tsv	Thu Oct 04 09:48:26 2018 -0400
+++ b/test-data/noclass.merged.sampleMetadata.tsv	Fri Nov 09 15:26:30 2018 -0500
@@ -1,4 +1,4 @@
-sampleMetadata	class
+sample_name	class
 ko15	.
 ko16	.
 wt15	.