intarna: intarna.xml annotate

annotate intarna.xml @ 8:0795d6cf0967 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6fa2a0294d615c9f267b766337dca0b2d3637219"

author	bgruening
date	Fri, 11 Oct 2019 18:37:19 -0400
parents	fd067a1143f3
children	56f1cef52e96

rev	line source
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	1 <tool id="intarna" name="IntaRNA" version="3.1.1">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	3 <macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	4 <macro name="query_macro">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	6 <conditional name="qAcc_cond">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	8 <option value="N">No accessibility contributions ('N')</option>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	12 </param>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	13 <when value="N" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	14 <when value="C" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	15 <when value="P">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	16 <param argument="--qAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	17 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	18 <when value="E">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	19 <param argument="--qAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	20 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	21 </conditional>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	22 <param argument="--qAccW" help="... for query accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	23 <param argument="--qAccL" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	24 </macro>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	25 <macro name="target_macro">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	26 <param argument="--target" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	27 <conditional name="tAcc_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	29 <option value="N">No accessibility contributions ('N')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	33 </param>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	34 <when value="N" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	35 <when value="C" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	36 <when value="P">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	37 <param argument="--tAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	38 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	39 <when value="E">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	40 <param argument="--tAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	41 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	42 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	43 <param argument="--tAccW" help="... for target accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	44 <param argument="--tAccL" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	45 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	46 <macro name="seed_macro">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	48 <param argument="--seedBP" help="number of inter-molecular base pairs within the seed region" label="Min. number of basepairs in seed" max="20" min="2" type="integer" value="7" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	49 <param argument="--seedMaxUP" help="Maximal number of unpaired seed bases both in query and target" label="Max. overall number of unpaired bases in seed" max="10" min="0" type="integer" value="0" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	50 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	51 <macro name="interaction_macro">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	52 <param argument="--mode" help="" label="Prediction mode" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	53 <option selected="true" value="H">Heuristic ('H')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	54 <option value="M">Exact but slow ('M')</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	55 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	56 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	57 <macro name="output_macro">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	58 <param argument="--outCsvCols" help="An empty argument prints all possible columns from the following available ID list: [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]" label="Comma separated list of CSV column IDs to print" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	59 <param argument="--outCsvSort" help="One of the column IDs to be printed that is used to sort the CSV table output" label="Sort CSV output for the given column label from CSV column IDs to print" type="text" value="E" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	60 <param argument="--outNumber" help="Number of optimal and suboptimal interaction to predict per query-target pair" label="Max. number of predictions per query/target pair" max="1000" min="0" type="integer" value="1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	62 <option value="N">in none of the sequences</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	63 <option value="T">in the target only</option>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	64 <option selected="true" value="Q">in the query only</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	65 <option value="B">in both sequences</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	66 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	67 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	68 </macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	69 <requirements>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	70 <requirement type="package" version="3.1.1">intarna</requirement>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	71 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	72 <version_command>IntaRNA --version</version_command>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	73 <command detect_errors="exit_code"><![CDATA[
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	74
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	75 IntaRNA
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	76 #if $advancedOptions.advancedSelector == "advanced"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	77 ## Query parameters
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	78 --query '$advancedOptions.query.query'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	79 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	80 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	81 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	82 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	83 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	84 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	85 --qIntLoopMax $advancedOptions.query.qIntLoopMax
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	86 #if $advancedOptions.query.qRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	87 --qRegion '$advancedOptions.query.qRegion'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	88 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	89 ## Target param.
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	90 --target '$advancedOptions.target.target'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	91 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	92 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	93 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	94 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	95 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	96 --tAccL $advancedOptions.target.tAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	97 --tIntLoopMax $advancedOptions.target.tIntLoopMax
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	98 #if $advancedOptions.target.tRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	99 --tRegion '$advancedOptions.target.tRegion'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	100 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	101 ## Seed param.
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	102 #if $advancedOptions.seed.noSeed
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	103 $advancedOptions.seed.noSeed
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	104 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	105 --seedBP $advancedOptions.seed.seedBP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	106 --seedMaxE $advancedOptions.seed.seedMaxE
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	107 --seedMinPu $advancedOptions.seed.seedMinPu
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	108 #if $advancedOptions.seed.seedMaxUP > 0
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	109 --seedMaxUP $advancedOptions.seed.seedMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	110 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	111 #if $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	112 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	113 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	114 #if $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	115 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	116 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	117 #if $advancedOptions.seed.seedQRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	118 --seedQRange '$advancedOptions.seed.seedQRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	119 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	120 #if $advancedOptions.seed.seedTRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	121 --seedTRange '$advancedOptions.seed.seedTRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	122 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	123 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	124 ## SHAPE param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	125 #if $advancedOptions.shape.qShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	126 --qShape '$advancedOptions.shape.qShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	127 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	128 #if $advancedOptions.shape.tShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	129 --tShape '$advancedOptions.shape.tShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	130 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	131 ## Prediction param.
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	132 --mode $advancedOptions.interaction.mode
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	133 --model $advancedOptions.interaction.model
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	134 --energy V
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	135 --energyVRNA '$advancedOptions.interaction.energyVRNA'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	136 --temperature $advancedOptions.interaction.temperature
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	137 #if $advancedOptions.interaction.windowWidth
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	138 --windowWidth $advancedOptions.interaction.windowWidth
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	139 --windowOverlap $advancedOptions.interaction.windowOverlap
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	140 #end if
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	141
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	142 ##Output param.
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	143 ## create temporary output file to be converted to tab-separated output (see below)
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	144 --out STDOUT
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	145 --outMode C
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	146 --outCsvCols '$advancedOptions.output.outCsvCols'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	147 --outCsvSort '$advancedOptions.output.outCsvSort'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	148 --outNumber $advancedOptions.output.outNumber
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	149 --outOverlap $advancedOptions.output.outOverlap
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	150 --outMaxE $advancedOptions.output.outMaxE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	151 --outDeltaE $advancedOptions.output.outDeltaE
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	152 ## add additional output files
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	153 #if $advancedOptions.output.add_output_cond.selector == "add"
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	154 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	155 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	156 #if $outFile == 'qAcc' or $outFile == 'tAcc'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	157 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	158 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	159 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	160 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	161 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	162 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	163 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	164 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	165 --out '$curOutFile'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	166 #end for
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	167 #end if
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	168 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	169 #elif $advancedOptions.advancedSelector == "basic"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	170 ## Query parameters
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	171 --query '$advancedOptions.query.query'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	172 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	173 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	174 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	175 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	176 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	177 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	178 ## Target param.
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	179 --target '$advancedOptions.target.target'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	180 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	183 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	184 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	185 --tAccL $advancedOptions.target.tAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	186 ## Seed param.
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	187 #if $advancedOptions.seed.noSeed
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	188 $advancedOptions.seed.noSeed
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	189 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	190 --seedBP $advancedOptions.seed.seedBP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	191 --seedMaxUP $advancedOptions.seed.seedMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	192 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	193 ## Prediction param.
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	194 --mode $advancedOptions.interaction.mode
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	195 ## Output param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	196 ## create temporary output file to be converted to tab-separated output (see below)
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	197 --out STDOUT
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	198 --outNumber $advancedOptions.output.outNumber
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	199 --outOverlap $advancedOptions.output.outOverlap
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	200 --outMode C
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	201 --outCsvCols '$advancedOptions.output.outCsvCols'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	202 --outCsvSort '$advancedOptions.output.outCsvSort'
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	203 #end if
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	204
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	205 ## Multithreading param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	206 --threads "\${GALAXY_SLOTS:-1}"
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	207 ## convert semicolon-separated output to tab-separated file
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	208 \| sed 's/\t/ /g' \| sed 's/;/\t/g' > '$outfile'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	209 ## convert additional semicolon-separated output to tab-separated file
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	210 #if $advancedOptions.advancedSelector == "advanced"
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	211 #if $advancedOptions.output.add_output_cond.selector == "add"
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	212 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	213 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	214 #if $outFile != 'qAcc' and $outFile != 'tAcc' and $outFile != 'qPu' and $outFile != 'tPu'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	215 #set curOutFile = 'intarna_' + str($outFile) + '*.tabular'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	216 && sed -i 's/\t/ /g' $curOutFile
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	217 && sed -i 's/;/\t/g' $curOutFile
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	218 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	219 #end for
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	220 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	221 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	222 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	223 ]]>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	224 </command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	225 <inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	226 <conditional name="advancedOptions">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	227 <param label="Options" name="advancedSelector" type="select">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	228 <option value="basic">Basic Options</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	229 <option value="advanced">Advanced Options</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	230 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	231 <when value="advanced">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	232 <section expanded="True" name="query" title="Query Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	233 <expand macro="query_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	234 <param argument="--qIntLoopMax" help="... to be considered in interactions within the query" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	235 <param argument="--qRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Query regions to be considered for interaction prediction" optional="true" type="text" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	236 </section>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	237 <section expanded="True" name="target" title="Target Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	238 <expand macro="target_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	239 <param argument="--tIntLoopMax" help="... to be considered in interactions within the target" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	240 <param argument="--tRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Target regions to be considered for interaction prediction" optional="true" type="text" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	241 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	242 <section name="seed" title="Seed Parameters">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	243 <expand macro="seed_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	244 <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	245 <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	246 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	247 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	248 <param argument="--seedQRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the query to search for seeds" optional="true" type="text" value="" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	249 <param argument="--seedTRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the target to search for seeds" optional="true" type="text" value="" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	250 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	251 <section name="shape" title="SHAPE Input Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	252 <param argument="--qShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	253 <param argument="--tShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	254 </section>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	255 <section name="interaction" title="Prediction Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	256 <expand macro="interaction_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	257 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	258 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	259 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	260 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	261 </param>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	262 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	263 <option value="Turner99">Turner-1999</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	264 <option selected="true" value="Turner04">Turner-2004</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	265 <option value="Andronescu07">Andronescu-2007</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	266 </param>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	267 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	268 <param argument="--windowWidth" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA." label="Window-based computation: window width" max="99999" min="10" optional="True" type="integer" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	269 <param argument="--windowOverlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target." label="Window-based computation: window overlap" max="99999" min="10" type="integer" value="150" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	270 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	271 <section name="output" title="Output Options">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	272 <expand macro="output_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	273 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	274 <param argument="--outDeltaE" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported" label="Max. delta energy above mfe of an interaction" type="float" value="100" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	275 <conditional name="add_output_cond">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	276 <param label="Additional output files" name="selector" type="select">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	277 <option value="add">Output additional files</option>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	278 <option selected="true" value="none">Don't output additional files</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	279 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	280 <when value="add">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	281 <param display="checkboxes" help="Written in a format similar to RNAplfold unpaired probability output." label="Additional output files" multiple="True" name="add_output" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	282 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	283 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	284 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	285 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	286 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	287 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	288 <option value="qAcc">The query's ED values (qAcc)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	289 <option value="tAcc">The target's ED values (tAcc) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	290 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	291 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	292 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	293 </when>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	294 <when value="none" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	295 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	296 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	297 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	298 <when value="basic">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	299 <section expanded="True" name="query" title="Query Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	300 <expand macro="query_macro" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	301 </section>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	302 <section expanded="True" name="target" title="Target Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	303 <expand macro="target_macro" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	304 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	305 <section name="seed" title="Seed Parameters">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	306 <expand macro="seed_macro" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	307 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	308 <section name="interaction" title="Interaction Parameters">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	309 <expand macro="interaction_macro" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	310 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	311 <section name="output" title="Output Options">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	312 <expand macro="output_macro" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	313 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	314 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	315 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	316 </inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	317 <outputs>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	318 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	319 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	320 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	321 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	322 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	323 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	324 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	325 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	326 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	327 <discover_datasets format="tabular" pattern="intarna_(?P<designation>spotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	328 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	329 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	330 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	331 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	332 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	333 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	334 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	335 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	336 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	337 <discover_datasets format="tabular" pattern="intarna_(?P<designation>qSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	338 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	339 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	340 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	341 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	342 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	343 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	344 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	345 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	346 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	347 <discover_datasets format="tabular" pattern="intarna_(?P<designation>tSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	348 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	349 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	350 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	351 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	352 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	353 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	354 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	355 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	356 </filter>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	357 <discover_datasets format="tabular" pattern="intarna_(?P<designation>qMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	358 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	359 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	360 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	361 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	362 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	363 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	364 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	365 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	366 </filter>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	367 <discover_datasets format="tabular" pattern="intarna_(?P<designation>tMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	368 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	369 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	370 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	371 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	372 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	373 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	374 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	375 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	376 </filter>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	377 <discover_datasets format="tabular" pattern="intarna_(?P<designation>pMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	378 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	379 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	380 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	381 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	382 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	383 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	384 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	385 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	386 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	387 <discover_datasets format="txt" pattern="intarna_(?P<designation>qAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	388 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	389 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	390 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	391 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	392 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	393 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	394 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	395 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	396 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	397 <discover_datasets format="txt" pattern="intarna_(?P<designation>tAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	398 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	399 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	400 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	401 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	402 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	403 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	404 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	405 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	406 </filter>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	407 <discover_datasets format="txt" pattern="intarna_(?P<designation>qPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	408 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	409 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	410 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	411 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	412 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	413 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	414 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	415 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	416 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	417 <discover_datasets format="txt" pattern="intarna_(?P<designation>tPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	418 </collection>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	419 </outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	420 <tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	421 <test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	422 <conditional name="advancedOptions">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	423 <param name="advancedSelector" value="basic" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	424 <section name="query">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	425 <param name="query" value="intarna_query.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	426 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	427 <section name="target">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	428 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	429 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	430 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	431 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	432 </test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	433 <test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	434 <conditional name="advancedOptions">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	435 <param name="advancedSelector" value="advanced" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	436 <section name="query">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	437 <param name="query" value="intarna_query.fa" />
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	438 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	439 <section name="target">
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	440 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	441 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	442 <section name="output">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	443 <conditional name="add_output_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	444 <param name="selector" value="add" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	445 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	446 </conditional>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	447 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	448 </conditional>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	449 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	450 <output_collection count="4" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	451 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	452 <output_collection count="4" name="qMinE_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	453 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	454 <output_collection count="2" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	455 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	456 <output_collection count="2" name="tAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	457 </output_collection>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	458 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	459 </tests>
7 fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc" bgruening parents: 6 diff changeset	460 <help><![CDATA[
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	461
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	462 What it does
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	463 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	464 During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	465 IntaRNA, developed by `Prof. Backofen's bioinformatics group at Freiburg University <http://www.bioinf.uni-freiburg.de/>`_, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	466 .. class:: infomark
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	467 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	468 Input
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	469 RNA sequences in FASTA format
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	470 Output
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	471 RNA-RNA interaction information in CSV format and additional information/files on demand
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	472
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	473 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	474 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	475 <citations>
3 03c09b961567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d rnateam parents: 2 diff changeset	476 <citation type="doi">10.1093/nar/gkx279</citation>
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	477 <citation type="doi">10.1093/nar/gku359</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	478 <citation type="doi">10.1093/bioinformatics/btn544</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	479 </citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	480 </tool>

Mercurial > repos > rnateam > intarna

annotate intarna.xml @ 8:0795d6cf0967 draft