diff averageFragSpectra.xml @ 12:e0b1da3ed06b draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea

--- a/averageFragSpectra.xml	Thu Jun 27 12:32:08 2019 -0400
+++ b/averageFragSpectra.xml	Fri Sep 13 11:52:29 2019 -0400
@@ -33,31 +33,14 @@
         <param name="pa" type="data" label="purityA object" format="rdata"
                help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
 
-        <conditional name="av">
-            <param name="level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
-                <option value="intra" selected="true">within a MS data file</option>
-                <option value="inter">accross MS data files</option>
-                <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
-            </param>
-            <when value="intra">
-                <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
-                <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
-            </when>
-            <when value="inter">
-                <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
-                <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
-            </when>
-            <when value="all">
-                <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
-                <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
-            </when>
-        </conditional>
 
         <param name="av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
             <option value="intra" selected="true">within a MS data file</option>
-            <option value="inter">accross MS data files</option>
-            <option value="all">within and accross MS data files (ignoring intra and inter relationships)</option>
+            <option value="inter">across MS data files</option>
+            <option value="all">within and across MS data files (ignoring intra and inter relationships)</option>
         </param>
+
+
         <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
         <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
         <param name="minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />