this time, I add the zip param

workflow4metabolomics · Jun 1, 2016 · 182e57f · 182e57f
1 parent dc5427a
commit 182e57f
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Showing 4 changed files with 28 additions and 15 deletions.
diff --git a/galaxy/probmetab/ProbMetab.xml b/galaxy/probmetab/ProbMetab.xml
@@ -38,6 +38,10 @@
         #end if
         allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol
         opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob
+
+        #if $zip_file:
+            zipfile $zip_file
+        #end if
 
     </command>
 
@@ -155,7 +159,10 @@
             <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms).
 " />
 
-        -->
+         -->
+
+        <!-- To pass planemo test -->
+        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
 
     </inputs>
 
@@ -190,6 +197,7 @@
         <test>
             <param name="acquisition_options|mode" value="one" />
             <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
+            <param name="zip_file" value="faahKO_reduce.zip"  ftype="zip" />
             <output name="log">
                 <assert_contents>
                     <has_text text="ko15 ko16 wt15 wt16" />
@@ -199,14 +207,6 @@
                     <has_text text="Step 4... compute q-values and local fdr" />
                 </assert_contents>
             </output>
-
-
-
-
-
-
-
-        DONE
         </test>
     </tests>
 

diff --git a/galaxy/probmetab/probmetab.r b/galaxy/probmetab/probmetab.r
@@ -27,9 +27,7 @@ cat("\tARGUMENTS INFO\n")
 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
 
-if (!is.null(listArguments[["zipfile"]])){
-  zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
-}
+
 
 # ----- PROCESSING INFILE -----
 cat("\tINFILE PROCESSING INFO\n")
@@ -38,7 +36,12 @@ cat("\tINFILE PROCESSING INFO\n")
 
 if(listArguments[["mode_acquisition"]]=="one") {
 	load(listArguments[["xa"]])
-	#Unzip the chromatograms file for plotting EIC pour the HTML file
+
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+
+    #Unzip the chromatograms file for plotting EIC pour the HTML file
 	if(exists("zipfile"))
 	{
 		if (zipfile!=""){
@@ -53,6 +56,11 @@ if(listArguments[["mode_acquisition"]]=="one") {
 
 } else if(listArguments[["inputs_mode"]]=="two"){
 	load(listArguments[["image_pos"]])
+
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+
 	#Unzip the chromatograms file for plotting EIC pour the HTML file
 	if(exists("zipfile")) {
 		if (zipfile!=""){
@@ -69,6 +77,11 @@ if(listArguments[["mode_acquisition"]]=="one") {
 
 
 	load(listArguments[["image_neg"]])
+
+    if (!is.null(listArguments[["zipfile"]])){
+        zipfile= listArguments[["zipfile"]]; listArguments[["zipfile"]]=NULL
+    }
+
 	#Unzip the chromatograms file for plotting EIC pour the HTML file
 	if(exists("zipfile")) {