# HG changeset patch
# User lecorguille
# Date 1488460804 18000
# Node ID dc4d3e2b9968a312cab87fd1c3b2f45d8ecfc802
# Parent  d8915395681fb4a8dba95ff0f5fad9c07c06f7fc
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312

diff -r d8915395681f -r dc4d3e2b9968 abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Wed Mar 01 16:56:01 2017 -0500
+++ b/abims_xcms_xcmsSet.xml	Thu Mar 02 08:20:04 2017 -0500
@@ -163,17 +163,18 @@
     </inputs>
 
     <outputs>
-        <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
-        <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
-        <data name="ticsRawPdf"   format="pdf" label="xset.TICs_raw.pdf" />
-        <data name="bpcsRawPdf"   format="pdf" label="xset.BPCs_raw.pdf" />
-        <data name="log" format="txt" label="xset.log.txt" />
+        <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
+        <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
+            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
+        </data>
+        <data name="ticsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
+        <data name="bpcsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
+        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
     </outputs>
 
     <tests>
         <!--<test>
-            <param name="inputs|input" value="zip_file" />
-            <param name="inputs|zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
+            <param name="input" value="sacuri_dir_root.zip"  ftype="zip" />
             <param name="methods|method" value="matchedFilter" />
             <param name="methods|step" value="0.01" />
             <param name="methods|fwhm" value="4" />
@@ -193,8 +194,7 @@
             </output>
         </test>
         <test>
-            <param name="inputs|input" value="zip_file" />
-            <param name="inputs|zip_file" value="sacuri_current_root.zip"  ftype="zip" />
+            <param name="input" value="sacuri_current_root.zip"  ftype="zip" />
             <param name="methods|method" value="centWave" />
             <param name="methods|ppm" value="25" />
             <param name="methods|peakwidth" value="20,50" />
@@ -227,8 +227,7 @@
         </test>
         <!-- Passed but disable to save time for Travis" -->
         <!--<test>
-            <param name="inputs|input" value="single_file" />
-            <param name="inputs|single_file" value="ko15.CDF"  ftype="netcdf" />
+            <param name="input" value="ko15.CDF"  ftype="netcdf" />
             <param name="methods|method" value="centWave" />
             <param name="methods|ppm" value="25" />
             <param name="methods|peakwidth" value="20,50" />
@@ -244,8 +243,7 @@
             </output>
         </test>
         <test>
-            <param name="inputs|input" value="single_file" />
-            <param name="inputs|single_file" value="ko16.CDF"  ftype="netcdf" />
+            <param name="input" value="ko16.CDF"  ftype="netcdf" />
             <param name="methods|method" value="centWave" />
             <param name="methods|ppm" value="25" />
             <param name="methods|peakwidth" value="20,50" />
@@ -261,8 +259,7 @@
             </output>
         </test>
         <test>
-            <param name="inputs|input" value="single_file" />
-            <param name="inputs|single_file" value="wt15.CDF"  ftype="netcdf" />
+            <param name="input" value="wt15.CDF"  ftype="netcdf" />
             <param name="methods|method" value="centWave" />
             <param name="methods|ppm" value="25" />
             <param name="methods|peakwidth" value="20,50" />
diff -r d8915395681f -r dc4d3e2b9968 xcms.r
--- a/xcms.r	Wed Mar 01 16:56:01 2017 -0500
+++ b/xcms.r	Thu Mar 02 08:20:04 2017 -0500
@@ -161,6 +161,11 @@
 cat("\t\tCOMPUTE\n")
 xset = do.call(thefunction, listArguments)
 
+# check if there are no peaks
+if (nrow(peaks(xset)) == 0) {
+    stop("No peaks were detected. You should review your settings")
+}
+
 
 cat("\n\n")
 
@@ -170,7 +175,6 @@
 
     #transform the files absolute pathways into relative pathways
     xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths)
-    print(zipfile)
     if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) {
 
         #Modify the samples names (erase the path)