diff LowMemPeakPickerHiRes.xml @ 1:c9c2a39c94de draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/LowMemPeakPickerHiRes.xml	Wed Mar 01 12:55:22 2017 -0500
+++ b/LowMemPeakPickerHiRes.xml	Wed Aug 09 09:53:58 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="LowMemPeakPickerHiRes" name="LowMemPeakPickerHiRes" version="2.1.0">
+<tool id="LowMemPeakPickerHiRes" name="LowMemPeakPickerHiRes" version="2.2.0">
   <description>Finds mass spectrometric peaks in profile mass spectra.</description>
   <macros>
     <token name="@EXECUTABLE@">LowMemPeakPickerHiRes</token>
@@ -36,7 +36,12 @@
   -algorithm:report_FWHM
 #end if
 #if $param_algorithm_report_FWHM_unit:
-  -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
+  -algorithm:report_FWHM_unit
+  #if " " in str($param_algorithm_report_FWHM_unit):
+    "$param_algorithm_report_FWHM_unit"
+  #else
+    $param_algorithm_report_FWHM_unit
+  #end if
 #end if
 #if $param_algorithm_SignalToNoise_win_len:
   -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
@@ -48,7 +53,12 @@
   -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
 #end if
 #if $param_algorithm_SignalToNoise_write_log_messages:
-  -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
+  -algorithm:SignalToNoise:write_log_messages
+  #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
+    "$param_algorithm_SignalToNoise_write_log_messages"
+  #else
+    $param_algorithm_SignalToNoise_write_log_messages
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -82,9 +92,9 @@
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
-    <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
+    <param name="param_algorithm_signal_to_noise" type="float" min="0.0" optional="True" value="0.0" label="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" help="(-signal_to_noise) "/>
     <repeat name="rep_param_algorithm_ms_levels" min="0" max="1" title="param_algorithm_ms_levels">
-      <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1 2" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
+      <param name="param_algorithm_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="List of MS levels for which the peak picking is applied" help="(-ms_levels) Other scans are copied to the output without changes">
         <sanitizer>
           <valid initial="string.printable">
             <remove value="'"/>
@@ -94,9 +104,9 @@
       </param>
     </repeat>
     <param name="param_algorithm_report_FWHM" display="radio" type="boolean" truevalue="-algorithm:report_FWHM" falsevalue="" checked="false" optional="True" label="Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak" help="(-report_FWHM) "/>
-    <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative(ppm)" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
+    <param name="param_algorithm_report_FWHM_unit" display="radio" type="select" optional="False" value="relative" label="Unit of FWHM. Either absolute in the unit of input," help="(-report_FWHM_unit) e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms)">
+      <option value="relative" selected="true">relative</option>
       <option value="absolute">absolute</option>
-      <option value="relative(ppm)" selected="true">relative(ppm)</option>
     </param>
     <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
     <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
@@ -123,5 +133,5 @@
   <help>Finds mass spectrometric peaks in profile mass spectra.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_LowMemPeakPickerHiRes.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_LowMemPeakPickerHiRes.html</help>
 </tool>