Mercurial > repos > tomnl > frag4feature

diff frag4feature.xml @ 28:07e3b8fb7c14 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a598583947118bd50cfe5ae12d955c20d6e502a6
author tomnl
date Tue, 17 Jul 2018 12:25:26 -0400
parents e2015e4f42be
children
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line diff
--- a/frag4feature.xml	Thu Jun 14 09:06:26 2018 -0400
+++ b/frag4feature.xml	Tue Jul 17 12:25:26 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="frag4feature" name="frag4feature" version="0.0.19">
+<tool id="frag4feature" name="frag4feature" version="0.0.20">
     <description>
         Assign fragmentation spectra to XCMS features using msPurity
     </description>
@@ -34,6 +34,10 @@
                 #end for
                 '
             #end if
+            #if $use_group
+                --use_group
+            #end if
+
             --ppm=$ppm_f4f
             --plim=$plim_f4f
             #if $mostIntense_f4f
@@ -42,7 +46,7 @@
             #if $convert2RawRT_f4f
                 --convert2RawRT
             #end if
- 	    #if $createDB
+ 	        #if $createDB
                 --createDB
             #end if
 
@@ -61,6 +65,10 @@
         <param name="mostIntense_f4f" type="boolean" checked="true" label="For matching fragmentation to a feature,
          use most intense peak within isolation window for precursor?"/>
 
+        <param name="use_group" type="boolean" checked="false" label="For matching fragmentation to a feature,
+         use the grouped feature range" help="If the MS1 and MS2 are in different files this is option has to be set to true"
+         />
+
         <param name="convert2RawRT_f4f" type="boolean" checked="false" label="Was retention time correction used?"
                help="If retention time correction has been used in XCMS set this to yes"/>