Mercurial > repos > rnateam > intarna
changeset 9:56f1cef52e96 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
| author | bgruening |
|---|---|
| date | Wed, 30 Oct 2019 12:30:28 -0400 |
| parents | 0795d6cf0967 |
| children | a3d8b6b2ffd8 |
| files | intarna.xml test-data/_intarna_result.tabular |
| diffstat | 2 files changed, 33 insertions(+), 81 deletions(-) [+] |
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--- 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>
--- 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