Repository 'intarna'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/intarna

Changeset 9:56f1cef52e96 (2019-10-30)
Previous changeset 8:0795d6cf0967 (2019-10-11) Next changeset 10:a3d8b6b2ffd8 (2019-11-04)
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
modified:
intarna.xml
removed:
test-data/_intarna_result.tabular
b
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
[
b'@@ -1,4 +1,4 @@\n-<tool id="intarna" name="IntaRNA" version="3.1.1">\n+<tool id="intarna" name="IntaRNA" version="3.1.2">\n     <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>\n     <macros>\n         <macro name="query_macro">\n@@ -67,13 +67,15 @@\n         </macro>\n     </macros>\n     <requirements>\n-        <requirement type="package" version="3.1.1">intarna</requirement>\n+        <requirement type="package" version="3.1.2">intarna</requirement>\n     </requirements>\n     <version_command>IntaRNA --version</version_command>\n     <command detect_errors="exit_code"><![CDATA[\n     \n         IntaRNA\n-            #if $advancedOptions.advancedSelector == "advanced"\n+            ## Multithreading\n+                --threads "\\${GALAXY_SLOTS:-1}"\n+            ## basic general parameters\n                 ## Query parameters\n                 --query \'$advancedOptions.query.query\'\n                 --qAcc $advancedOptions.query.qAcc_cond.qAcc\n@@ -82,10 +84,6 @@\n                 #end if\n                 --qAccW $advancedOptions.query.qAccW\n                 --qAccL $advancedOptions.query.qAccL\n-                --qIntLoopMax $advancedOptions.query.qIntLoopMax\n-                #if $advancedOptions.query.qRegion\n-                    --qRegion \'$advancedOptions.query.qRegion\'\n-                #end if\n                 ## Target param.\n                 --target \'$advancedOptions.target.target\'\n                 --tAcc $advancedOptions.target.tAcc_cond.tAcc\n@@ -94,20 +92,41 @@\n                 #end if\n                 --tAccW $advancedOptions.target.tAccW\n                 --tAccL $advancedOptions.target.tAccL\n+                ## Seed param.\n+                #if $advancedOptions.seed.noSeed\n+                    $advancedOptions.seed.noSeed\n+                #else\n+                    --seedBP $advancedOptions.seed.seedBP\n+                    #if $advancedOptions.seed.seedMaxUP > 0\n+                        --seedMaxUP $advancedOptions.seed.seedMaxUP\n+                    #end if\n+                #end if\n+                ## Prediction param.\n+                --mode $advancedOptions.interaction.mode\n+                --energy V\n+                ## Output param.\n+                --out $outfile\n+                --outMode C\n+                --outSep "`printf "\\t"`"\n+                --outNumber $advancedOptions.output.outNumber\n+                --outOverlap $advancedOptions.output.outOverlap\n+                --outCsvCols \'$advancedOptions.output.outCsvCols\'\n+                --outCsvSort \'$advancedOptions.output.outCsvSort\'\n+            #if $advancedOptions.advancedSelector == "advanced"\n+                ## Query parameters\n+                --qIntLoopMax $advancedOptions.query.qIntLoopMax\n+                #if $advancedOptions.query.qRegion\n+                    --qRegion \'$advancedOptions.query.qRegion\'\n+                #end if\n+                ## Target param.\n                 --tIntLoopMax $advancedOptions.target.tIntLoopMax\n                 #if $advancedOptions.target.tRegion\n                     --tRegion \'$advancedOptions.target.tRegion\'\n                 #end if\n                 ## Seed param.\n-                #if $advancedOptions.seed.noSeed\n-                    $advancedOptions.seed.noSeed\n-                #else\n-                    --seedBP $advancedOptions.seed.seedBP\n+                #if not $advancedOptions.seed.noSeed\n                     --seedMaxE $advancedOptions.seed.seedMaxE\n                     --seedMinPu $advancedOptions.seed.seedMinPu\n-                    #if $advancedOptions.seed.seedMaxUP > 0\n-                        --seedMaxUP $advancedOptions.seed.seedMaxUP\n-                    #end if\n                     #if $advancedOptions.seed.seedQMaxUP\n                         --seedQMaxUP $advancedOptions.seed.seedQMaxUP\n                     #end if\n@@ -129,24 +148,14 @@\n                     --tShape \'$advancedOptions.shape.tShape\'\n                 #end if\n            '..b're\n                 #if $advancedOptions.interaction.windowWidth\n                     --windowWidth $advancedOptions.interaction.windowWidth\n                     --windowOverlap $advancedOptions.interaction.windowOverlap\n                 #end if\n-                \n                 ##Output param.\n-                 ## create temporary output file to be converted to tab-separated output (see below)\n-                --out STDOUT\n-                --outMode C\n-                --outCsvCols \'$advancedOptions.output.outCsvCols\'\n-                --outCsvSort \'$advancedOptions.output.outCsvSort\'\n-                --outNumber $advancedOptions.output.outNumber\n-                --outOverlap $advancedOptions.output.outOverlap\n                 --outMaxE $advancedOptions.output.outMaxE\n                 --outDeltaE $advancedOptions.output.outDeltaE\n                 ## add additional output files\n@@ -166,59 +175,6 @@\n                     #end for\n                   #end if\n                 #end if\n-            #elif $advancedOptions.advancedSelector == "basic"\n-                ## Query parameters\n-                --query \'$advancedOptions.query.query\'\n-                --qAcc $advancedOptions.query.qAcc_cond.qAcc\n-                #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"\n-                    --qAccFile \'$advancedOptions.query.qAcc_cond.qAccFile\'\n-                #end if\n-                --qAccW $advancedOptions.query.qAccW\n-                --qAccL $advancedOptions.query.qAccL\n-                ## Target param.\n-                --target \'$advancedOptions.target.target\'\n-                --tAcc $advancedOptions.target.tAcc_cond.tAcc\n-                #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"\n-                    --tAccFile \'$advancedOptions.target.tAcc_cond.tAccFile\'\n-                #end if\n-                --tAccW $advancedOptions.target.tAccW\n-                --tAccL $advancedOptions.target.tAccL\n-                ## Seed param.\n-                #if $advancedOptions.seed.noSeed\n-                    $advancedOptions.seed.noSeed\n-                #else\n-                    --seedBP $advancedOptions.seed.seedBP\n-                    --seedMaxUP $advancedOptions.seed.seedMaxUP\n-                #end if\n-                ## Prediction param.\n-                --mode $advancedOptions.interaction.mode\n-                ## Output param.\n-                ## create temporary output file to be converted to tab-separated output (see below)\n-                --out STDOUT\n-                --outNumber $advancedOptions.output.outNumber\n-                --outOverlap $advancedOptions.output.outOverlap\n-                --outMode C\n-                --outCsvCols \'$advancedOptions.output.outCsvCols\'\n-                --outCsvSort \'$advancedOptions.output.outCsvSort\'\n-            #end if\n-            \n-            ## Multithreading param.\n-            --threads "\\${GALAXY_SLOTS:-1}"\n-            ## convert semicolon-separated output to tab-separated file\n-            | sed \'s/\\t/    /g\' | sed \'s/;/\\t/g\' > \'$outfile\'\n-            ## convert additional semicolon-separated output to tab-separated file\n-            #if $advancedOptions.advancedSelector == "advanced"\n-              #if $advancedOptions.output.add_output_cond.selector == "add"\n-                #if str($advancedOptions.output.add_output_cond.add_output.value) != \'None\'\n-                  #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:\n-                    #if $outFile != \'qAcc\' and $outFile != \'tAcc\' and $outFile != \'qPu\' and $outFile != \'tPu\'\n-                      #set curOutFile = \'intarna_\' + str($outFile) + \'*.tabular\'\n-                      && sed -i \'s/\\t/    /g\' $curOutFile\n-                      && sed -i \'s/;/\\t/g\' $curOutFile\n-                    #end if\n-                  #end for\n-                #end if\n-              #end if\n             #end if\n ]]>  \n     </command>\n'
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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
b
@@ -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