diff process_scans.xml @ 1:769165c75514 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06

--- a/process_scans.xml	Tue Feb 27 14:04:01 2018 -0500
+++ b/process_scans.xml	Wed May 30 09:20:20 2018 -0400
@@ -4,36 +4,36 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command><![CDATA[
+    <command detect_errors="exit_code">
+    <![CDATA[
         #if $input.format == "data_collection"
             #for $fn in $input.source
                 #if str( $fn ).endswith(".dat")
-                    ln -s "$fn" "$fn.name"
+                    ln -s '$fn' '$fn.name'
             	    &&
                 #end if
             #end for
         #elif $input.format == "single_file"
             #if str( $input.source ).endswith(".dat")
-                ln -s "$input.source" "$input.source.name"
+                ln -s '$input.source' '$input.source.name'
                 &&
             #end if
         #end if
         dimspy process-scans
         #if $input.format == "data_collection"
             #for $fn in $input.source
-                --input "$fn.name"
+                --input '$fn.name'
             #end for
         #elif $input.format == "single_file"
-            --input "$input.source.name"
+            --input '$input.source.name'
         #elif $input.format == "library"
-            --input $__app__.config.user_library_import_dir/$__user_email__/$input.source
+            --input '$__app__.config.user_library_import_dir/$__user_email__/$input.source'
         #else
-            --input "$input.source"
+            --input '$input.source'
         #end if
-        --output "$hdf5_file_out"
+        --output '$hdf5_file_out'
         #if $filelist
-            --filelist "$filelist"
+            --filelist '$filelist'
         #end if
         --function-noise $function_noise
         --snr-threshold $snr_threshold
@@ -51,7 +51,7 @@
             --skip-stitching
         #end if
         #if float($adv.ringing_threshold) > 0.0
-            --ringing_threshold $adv.ringing_threshold
+            --ringing-threshold $adv.ringing_threshold
         #end if
         #for $mzr in $adv.remove_mz_range
             --remove-mz-range $mzr.start $mzr.end
@@ -65,13 +65,14 @@
                 #end if
             #end for
         #end if
-        --report "$report"
+        --report '$report'
         &&
         dimspy hdf5-pls-to-txt
-        --input "$hdf5_file_out"
+        --input '$hdf5_file_out'
         --output .
         --delimiter $delimiter
-    ]]></command>
+    ]]>
+    </command>
     <inputs>
         <conditional name="input">
             <param name="format" type="select" label="Choose the source for the dataset" >