diff align_samples.xml @ 1:a941ec0fd2a4 draft default tip

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

--- a/align_samples.xml	Tue Feb 27 14:01:25 2018 -0500
+++ b/align_samples.xml	Wed May 30 09:16:29 2018 -0400
@@ -4,13 +4,13 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command><![CDATA[
+    <command detect_errors="exit_code">
+    <![CDATA[
         dimspy align-samples
-        --input "$hdf5_file_in"
-        --output "$hdf5_file_out"
+        --input '$hdf5_file_in'
+        --output '$hdf5_file_out'
         #if $filelist
-            --filelist "$filelist"
+            --filelist '$filelist'
         #end if
         --ppm $ppm
         #if $hdf5_to_txt.standard
@@ -21,11 +21,12 @@
             &&
             @HDF5_PM_TO_TXT_COMPREHENSIVE@
         #end if
-    ]]></command>
+    ]]>
+    </command>
     <inputs>
         <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="" argument="--input"/>
-        <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" argument="--filelist"/>
-        <param name="ppm" type="float" value="2.0" label="ppm" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/>
+        <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for  Process Scans or Replicate Filter." argument="--filelist"/>
+        <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." argument="--ppm"/>
         <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
         <expand macro="hdf5_pm_to_txt" />
     </inputs>
@@ -93,7 +94,7 @@
 | A tabular-formatted .txt file with columns: filename, batch, classLabel, injectionOrder.
 | Additional collumns are allowed but are not used during processing.
 | This file must be uploaded in to (or available from) the current history in order to allow for it to be selected from the drop-down menu.
-| **NOTE:** Only provide a filelist if you like to exclude Peaklist or if you have not provided a filelist for 'Process Scans' or Replicate Filter'.
+| **NOTE:** Only provide a filelist if you like to exclude Peaklist, update the metadata (e.g. classLabel), or if you have not provided a filelist for 'Process Scans' or Replicate Filter'.
 | 
 	
 <![CDATA[