# HG changeset patch
# User bgruening
# Date 1572453028 14400
# Node ID 56f1cef52e96d9300293fc3b1fe35089a1452210
# Parent  0795d6cf096729eb049822ffdf33cb440393bf8f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"

diff -r 0795d6cf0967 -r 56f1cef52e96 intarna.xml
--- a/intarna.xml	Fri Oct 11 18:37:19 2019 -0400
+++ b/intarna.xml	Wed Oct 30 12:30:28 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="intarna" name="IntaRNA" version="3.1.1">
+<tool id="intarna" name="IntaRNA" version="3.1.2">
     <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
     <macros>
         <macro name="query_macro">
@@ -67,13 +67,15 @@
         </macro>
     </macros>
     <requirements>
-        <requirement type="package" version="3.1.1">intarna</requirement>
+        <requirement type="package" version="3.1.2">intarna</requirement>
     </requirements>
     <version_command>IntaRNA --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
     
         IntaRNA
-            #if $advancedOptions.advancedSelector == "advanced"
+            ## Multithreading
+                --threads "\${GALAXY_SLOTS:-1}"
+            ## basic general parameters
                 ## Query parameters
                 --query '$advancedOptions.query.query'
                 --qAcc $advancedOptions.query.qAcc_cond.qAcc
@@ -82,10 +84,6 @@
                 #end if
                 --qAccW $advancedOptions.query.qAccW
                 --qAccL $advancedOptions.query.qAccL
-                --qIntLoopMax $advancedOptions.query.qIntLoopMax
-                #if $advancedOptions.query.qRegion
-                    --qRegion '$advancedOptions.query.qRegion'
-                #end if
                 ## Target param.
                 --target '$advancedOptions.target.target'
                 --tAcc $advancedOptions.target.tAcc_cond.tAcc
@@ -94,20 +92,41 @@
                 #end if
                 --tAccW $advancedOptions.target.tAccW
                 --tAccL $advancedOptions.target.tAccL
+                ## Seed param.
+                #if $advancedOptions.seed.noSeed
+                    $advancedOptions.seed.noSeed
+                #else
+                    --seedBP $advancedOptions.seed.seedBP
+                    #if $advancedOptions.seed.seedMaxUP > 0
+                        --seedMaxUP $advancedOptions.seed.seedMaxUP
+                    #end if
+                #end if
+                ## Prediction param.
+                --mode $advancedOptions.interaction.mode
+                --energy V
+                ## Output param.
+                --out $outfile
+                --outMode C
+                --outSep "`printf "\t"`"
+                --outNumber $advancedOptions.output.outNumber
+                --outOverlap $advancedOptions.output.outOverlap
+                --outCsvCols '$advancedOptions.output.outCsvCols'
+                --outCsvSort '$advancedOptions.output.outCsvSort'
+            #if $advancedOptions.advancedSelector == "advanced"
+                ## Query parameters
+                --qIntLoopMax $advancedOptions.query.qIntLoopMax
+                #if $advancedOptions.query.qRegion
+                    --qRegion '$advancedOptions.query.qRegion'
+                #end if
+                ## Target param.
                 --tIntLoopMax $advancedOptions.target.tIntLoopMax
                 #if $advancedOptions.target.tRegion
                     --tRegion '$advancedOptions.target.tRegion'
                 #end if
                 ## Seed param.
-                #if $advancedOptions.seed.noSeed
-                    $advancedOptions.seed.noSeed
-                #else
-                    --seedBP $advancedOptions.seed.seedBP
+                #if not $advancedOptions.seed.noSeed
                     --seedMaxE $advancedOptions.seed.seedMaxE
                     --seedMinPu $advancedOptions.seed.seedMinPu
-                    #if $advancedOptions.seed.seedMaxUP > 0
-                        --seedMaxUP $advancedOptions.seed.seedMaxUP
-                    #end if
                     #if $advancedOptions.seed.seedQMaxUP
                         --seedQMaxUP $advancedOptions.seed.seedQMaxUP
                     #end if
@@ -129,24 +148,14 @@
                     --tShape '$advancedOptions.shape.tShape'
                 #end if
                 ## Prediction param.
-                --mode $advancedOptions.interaction.mode
                 --model $advancedOptions.interaction.model
-                --energy V
                 --energyVRNA '$advancedOptions.interaction.energyVRNA'
                 --temperature $advancedOptions.interaction.temperature
                 #if $advancedOptions.interaction.windowWidth
                     --windowWidth $advancedOptions.interaction.windowWidth
                     --windowOverlap $advancedOptions.interaction.windowOverlap
                 #end if
-                
                 ##Output param.
-                 ## create temporary output file to be converted to tab-separated output (see below)
-                --out STDOUT
-                --outMode C
-                --outCsvCols '$advancedOptions.output.outCsvCols'
-                --outCsvSort '$advancedOptions.output.outCsvSort'
-                --outNumber $advancedOptions.output.outNumber
-                --outOverlap $advancedOptions.output.outOverlap
                 --outMaxE $advancedOptions.output.outMaxE
                 --outDeltaE $advancedOptions.output.outDeltaE
                 ## add additional output files
@@ -166,59 +175,6 @@
                     #end for
                   #end if
                 #end if
-            #elif $advancedOptions.advancedSelector == "basic"
-                ## Query parameters
-                --query '$advancedOptions.query.query'
-                --qAcc $advancedOptions.query.qAcc_cond.qAcc
-                #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
-                    --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
-                #end if
-                --qAccW $advancedOptions.query.qAccW
-                --qAccL $advancedOptions.query.qAccL
-                ## Target param.
-                --target '$advancedOptions.target.target'
-                --tAcc $advancedOptions.target.tAcc_cond.tAcc
-                #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
-                    --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
-                #end if
-                --tAccW $advancedOptions.target.tAccW
-                --tAccL $advancedOptions.target.tAccL
-                ## Seed param.
-                #if $advancedOptions.seed.noSeed
-                    $advancedOptions.seed.noSeed
-                #else
-                    --seedBP $advancedOptions.seed.seedBP
-                    --seedMaxUP $advancedOptions.seed.seedMaxUP
-                #end if
-                ## Prediction param.
-                --mode $advancedOptions.interaction.mode
-                ## Output param.
-                ## create temporary output file to be converted to tab-separated output (see below)
-                --out STDOUT
-                --outNumber $advancedOptions.output.outNumber
-                --outOverlap $advancedOptions.output.outOverlap
-                --outMode C
-                --outCsvCols '$advancedOptions.output.outCsvCols'
-                --outCsvSort '$advancedOptions.output.outCsvSort'
-            #end if
-            
-            ## Multithreading param.
-            --threads "\${GALAXY_SLOTS:-1}"
-            ## convert semicolon-separated output to tab-separated file
-            | sed 's/\t/    /g' | sed 's/;/\t/g' > '$outfile'
-            ## convert additional semicolon-separated output to tab-separated file
-            #if $advancedOptions.advancedSelector == "advanced"
-              #if $advancedOptions.output.add_output_cond.selector == "add"
-                #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
-                  #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
-                    #if $outFile != 'qAcc' and $outFile != 'tAcc' and $outFile != 'qPu' and $outFile != 'tPu'
-                      #set curOutFile = 'intarna_' + str($outFile) + '*.tabular'
-                      && sed -i 's/\t/    /g' $curOutFile
-                      && sed -i 's/;/\t/g' $curOutFile
-                    #end if
-                  #end for
-                #end if
-              #end if
             #end if
 ]]>  
     </command>
diff -r 0795d6cf0967 -r 56f1cef52e96 test-data/_intarna_result.tabular
--- a/test-data/_intarna_result.tabular	Fri Oct 11 18:37:19 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-id1	start1	end1	id2	start2	end2	subseqDP	hybridDP	E
-mRNA1	85	95	ncRNA1	21	32	GUGGUGAGGAG&CUCCUCACACAC	(((((((((((&)))))))).)))	-11.8783
-mRNA1	52	58	ncRNA2	28	34	UCAGUUA&UGACUGA	(((((((&)))))))	-3.08648
-mRNA2	86	97	ncRNA1	20	31	UGUGUGACGAGU&ACUCCUCACACA	(((((((.((((&)))).)))))))	-8.16744