diff MRMTransitionGroupPicker.xml @ 3:4b87a29bf4e2 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

--- a/MRMTransitionGroupPicker.xml	Thu Apr 27 12:57:37 2017 -0400
+++ b/MRMTransitionGroupPicker.xml	Fri Jul 14 18:55:21 2017 -0400
@@ -1,7 +1,8 @@
 <?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="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.1.0">
+<tool id="MRMTransitionGroupPicker" name="MRMTransitionGroupPicker" version="2.2.0">
+  <description>Picks peaks in SRM/MRM chromatograms.</description>
   <macros>
     <token name="@EXECUTABLE@">MRMTransitionGroupPicker</token>
     <import>macros.xml</import>
@@ -90,7 +91,10 @@
   #end if
 #end if
     #if $adv_opts.param_algorithm_recalculate_peaks:
-  -algorithm:recalculate_peaks     "$adv_opts.param_algorithm_recalculate_peaks"
+  -algorithm:recalculate_peaks
+#end if
+    #if $adv_opts.param_algorithm_use_precursors:
+  -algorithm:use_precursors
 #end if
     #if $adv_opts.param_algorithm_recalculate_peaks_max_z:
   -algorithm:recalculate_peaks_max_z $adv_opts.param_algorithm_recalculate_peaks_max_z
@@ -99,7 +103,7 @@
   -algorithm:minimal_quality $adv_opts.param_algorithm_minimal_quality
 #end if
     #if $adv_opts.param_algorithm_compute_peak_quality:
-  -algorithm:compute_peak_quality     "$adv_opts.param_algorithm_compute_peak_quality"
+  -algorithm:compute_peak_quality
 #end if
 #end if
 </command>
@@ -137,31 +141,18 @@
         <option value="smoothed">smoothed</option>
         <option value="original">original</option>
       </param>
-      <param name="param_algorithm_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_recalculate_peaks" display="radio" type="boolean" truevalue="-algorithm:recalculate_peaks" falsevalue="" checked="false" optional="True" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large"/>
+      <param name="param_algorithm_use_precursors" display="radio" type="boolean" truevalue="-algorithm:use_precursors" falsevalue="" checked="false" optional="True" label="Use precursor chromatogram for peak picking" help="(-use_precursors) "/>
       <param name="param_algorithm_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
       <param name="param_algorithm_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
-      <param name="param_algorithm_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
-        <sanitizer>
-          <valid initial="string.printable">
-            <remove value="'"/>
-            <remove value="&quot;"/>
-          </valid>
-        </sanitizer>
-      </param>
+      <param name="param_algorithm_compute_peak_quality" display="radio" type="boolean" truevalue="-algorithm:compute_peak_quality" falsevalue="" checked="false" optional="True" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad"/>
     </expand>
   </inputs>
   <outputs>
     <data name="param_out" format="featurexml"/>
   </outputs>
-  <help>None
+  <help>Picks peaks in SRM/MRM chromatograms.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MRMTransitionGroupPicker.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MRMTransitionGroupPicker.html</help>
 </tool>