diff FeatureFinderMetabo.xml @ 9:b6e4da302f66 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 08:25:30 -0400
parents 1473223a9595
children 21dc135961b5
line wrap: on
line diff
--- a/FeatureFinderMetabo.xml	Tue Mar 20 14:52:17 2018 -0400
+++ b/FeatureFinderMetabo.xml	Wed May 15 08:25:30 2019 -0400
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>FeatureFinderMetabo
+  <command detect_errors="aggressive"><![CDATA[FeatureFinderMetabo
 
 #if $param_in:
   -in $param_in
@@ -88,7 +88,7 @@
   #end if
 #end if
 #if $param_algorithm_ffm_mz_scoring_13C:
-  -algorithm:ffm:mz_scoring_13C
+  -algorithm:ffm:mz_scoring_13C true
 #end if
 #if $param_algorithm_ffm_report_convex_hulls:
   -algorithm:ffm:report_convex_hulls
@@ -144,7 +144,7 @@
   #end if
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Centroided mzML file" help="(-in) "/>
     <param name="param_algorithm_common_noise_threshold_int" type="float" value="10.0" label="Intensity threshold below which peaks are regarded as noise" help="(-noise_threshold_int) "/>
@@ -179,6 +179,12 @@
       <option value="metabolites (5% RMS)" selected="true">metabolites (5% RMS)</option>
       <option value="peptides">peptides</option>
       <option value="none">none</option>
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
     </param>
     <param name="param_algorithm_ffm_mz_scoring_13C" display="radio" type="boolean" truevalue="-algorithm:ffm:mz_scoring_13C" falsevalue="" checked="false" optional="True" label="Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!)" help="(-mz_scoring_13C) Disable for general metabolites (as described in Kenar et al. 2014, MCP.)"/>
     <param name="param_algorithm_ffm_report_convex_hulls" display="radio" type="boolean" truevalue="-algorithm:ffm:report_convex_hulls" falsevalue="" checked="false" optional="True" label="Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably)" help="(-report_convex_hulls) "/>
@@ -211,5 +217,5 @@
   <help>Assembles metabolite features from centroided (LC-)MS data using the mass trace approach.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderMetabo.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureFinderMetabo.html</help>
 </tool>