# HG changeset patch
# User bgruening
# Date 1649778402 0
# Node ID ad8272078bde21c5761e78d7bba85ada23b12659
# Parent  80ecf7309850f6e67a74c1e52b21e9988318a238
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"

diff -r 80ecf7309850 -r ad8272078bde intarna.xml
--- a/intarna.xml	Mon Mar 02 21:17:50 2020 +0000
+++ b/intarna.xml	Tue Apr 12 15:46:42 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="intarna" name="IntaRNA" version="3.2.0">
+<tool id="intarna" name="IntaRNA" version="3.3.1">
     <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
     <macros>
         <macro name="query_macro">
@@ -64,10 +64,11 @@
                 <option selected="true" value="Q">in the query only</option>
                 <option value="B">in both sequences</option>
             </param>
+            <param argument="--outPairwise" checked="false" falsevalue="" help="" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" truevalue="--outPairwise" type="boolean" />
         </macro>
     </macros>
     <requirements>
-        <requirement type="package" version="3.2.0">intarna</requirement>
+        <requirement type="package" version="3.3.1">intarna</requirement>
     </requirements>
     <version_command>IntaRNA --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -112,6 +113,7 @@
                 --outOverlap $advancedOptions.output.outOverlap
                 --outCsvCols '$advancedOptions.output.outCsvCols'
                 --outCsvSort '$advancedOptions.output.outCsvSort'
+                $advancedOptions.output.outPairwise
             #if $advancedOptions.advancedSelector == "advanced"
                 ## Query parameters
                 --qIntLoopMax $advancedOptions.query.qIntLoopMax