diff replicate_filter.xml @ 1:9fc2f24615a7 draft default tip

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

--- a/replicate_filter.xml	Tue Feb 27 14:02:18 2018 -0500
+++ b/replicate_filter.xml	Wed May 30 09:17:44 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 replicate-filter
-        --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
         --replicates $replicates
@@ -18,23 +18,24 @@
         #if $rsd_threshold
             --rsd-threshold $rsd_threshold
         #end if
-        --report "$report"
+        --report '$report'
         &&
         dimspy create-sample-list
-        --input "$hdf5_file_out"
-        --output "$samplelist"
+        --input '$hdf5_file_out'
+        --output '$samplelist'
         --delimiter tab
         &&
         dimspy hdf5-pls-to-txt
-        --input "$hdf5_file_out"
+        --input '$hdf5_file_out'
         --output .
         --delimiter $delimiter
-    ]]></command>
+    ]]>
+    </command>
     <inputs>
         <param name="hdf5_file_in" type="data" format="h5" label="Peaklists (HDF5 file)" help="Peaklists generated by Process Scans (SIM-Stitch)." argument="--hdf5_file_in"/>
-        <param name="filelist" type="data" optional="true" format="tsv,tabular" label="Filelist / Samplelist" argument="--filelist" />
-        <param name="replicates" type="integer" value="3" label="Number of technical replicates" help="" argument="--replicates"/>
-        <param name="min_peaks" type="integer" value="2" label="Number of technical replicates a peak has to be present in" help="" argument="--min_peaks"/>
+        <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." argument="--filelist" />
+        <param name="replicates" type="integer" value="3" label="Number of technical replicates for each sample" help="" argument="--replicates"/>
+        <param name="min_peaks" type="integer" value="2" label="Minimum number of technical replicates a peak has to be present in" help="" argument="--min_peaks"/>
         <param name="ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across technical replicates in parts per million (ppm)." argument="--ppm"/>
         <param name="rsd_threshold" type="text" value="" label="Relative standard deviation threshold" help="Maximum tolerated relative standard deviation (RSD) of the peak intensities across technical replicates. Leave empty to skip this filter step." argument="--rsd-threshold"/>
         <param name="delimiter" type="hidden" value="tab" argument="--delimiter"/>
@@ -108,7 +109,7 @@
 | A tabular-formatted .txt file with columns: filename, replicate, 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'.
+| **NOTE:** 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'.
 | 
 
 @example_filelist@
@@ -117,7 +118,7 @@
    
 The total number of technical replicates acquired for each sample (all samples must have the same number of technical replicates)
 
-**\4. Number of technical replicates a peak has to be present in** (REQUIRED)
+**\4. Minimum number of technical replicates a peak has to be present in** (REQUIRED)
    
 A numerical value from 0 up to the numerical value entered in the 'Number of technical replicates' box. Peaks that occur in fewer than this number of technical replicates are removed from the output Peaklist.