Mercurial > repos > galaxyp > dia_umpire

diff dia_umpire_quant.xml @ 3:6caa9011f245 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire commit 2379480213ba2e084a93bf82052fac858ffd074f
author galaxyp
date Mon, 04 Mar 2019 11:49:18 -0500
parents e8f7be6a6e59
children
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--- a/dia_umpire_quant.xml	Mon Mar 19 16:40:29 2018 -0400
+++ b/dia_umpire_quant.xml	Mon Mar 04 11:49:18 2019 -0500
@@ -1,7 +1,7 @@
 <tool id="dia_umpire_quant" name="DIA_Umpire_Quant" version="@VERSION@.0">
     <description>DIA quantitation and targeted re-extraction</description>
     <macros>
-        <import>macros.xml</import>
+        <import>dia_umpire_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -23,7 +23,7 @@
 #end for
 ## Make sure pep.xml and prot.xml start with "interact-"
 ## && echo "# $quant_params" >> $dia_umpire_quant 
-&& dia_umpire_quant $quant_params 
+&& java -jar \$DIA_UMPIRE_QUANT_JAR $quant_params 
 && cp $work_path/ProtSummary*.xls "$ProtSummary"
 && cp $work_path/PeptideSummary*.xls "$PeptideSummary"
 && cp $work_path/FragSummary*.xls "$FragSummary"