intarna: intarna.xml annotate

author	rnateam
date	Tue, 21 Feb 2017 04:59:09 -0500
parents
children	34de9855c962

rev	line source
0 33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	1 <tool id="intarna" name="IntaRNA" version="2.0.0">
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">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	5 <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be 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	6 <conditional name="qAcc_cond">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	7 <param argument="--qAcc" type="select" label="Accessibility computation" help="">
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>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	9 <option value="C" selected="true">Computation of accessibilities ('C')</option>
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>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	13 <when value="N"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	14 <when value="C"/>
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">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	16 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />
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">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	19 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />
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>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	22 <param argument="--qAccW" type="integer" value="150" min="0" max="99999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	23 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	24 <param argument="--qAccL" type="integer" value="100" min="0" max="99999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	25 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	26 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	27 <macro name="target_macro">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	28 <param name="_target" argument="--target" format="fasta" type="data" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be 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	29 <conditional name="tAcc_cond">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	30 <param argument="--tAcc" type="select" label="Accessibility computation" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	31 <option value="N">No accessibility contributions ('N')</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	32 <option value="C" selected="true">Computation of accessibilities ('C')</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	33 <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	34 <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	35 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	36 <when value="N"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	37 <when value="C"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	38 <when value="P">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	39 <param argument="--tAccFile" format="text" type="data" label="The file to be parsed" help="... for accessibility computation" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	40 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	41 <when value="E">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	42 <param argument="--tAccFile" format="text" type="data" label="Accessibility computation" help="" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	43 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	44 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	45 <param argument="--tAccW" type="integer" value="150" min="0" max="99999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	49 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	50 <macro name="seed_macro">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	52 label="Disable seed constraint entirely for computation" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	55 label="Max. overall number of unpaired bases (query+target)" help=""/>
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="interaction_macro">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	58 <param argument="--mode" type="select" label="Prediction mode" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	59 <option value="H" selected="true">Heuristic (fast and low memory)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	60 <option value="M">Exact and low memory</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	61 <option value="E">Exact (high memory)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	62 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	63 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	64 <macro name="output_macro">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	65 <param argument="--outMode" type="select" label="Output Mode" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	66 <option value="N">Normal output (ASCII char + energy)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	67 <option value="D">Detailed output (ASCII char + energy/position details)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	68 <option value="C" selected="true">CSV output (see --outCsvCols)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	69 <option value="1">backward compatible IntaRNA v1.* normal output</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	70 <option value="O">backward compatible IntaRNA v1.* detailed output</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	71 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	72
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	73
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	74 <param argument="--outCsvCols" type="text" optional="true"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	75 label="Comma separated list of CSV column IDs to print" 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], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2]"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	76 <param argument="--outNumber" type="integer" value="1" min="0" max="1000"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	77 label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	78 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	79 <option value="N" >in none of the sequences</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	80 <option value="T">in the target only</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	81 <option value="Q" selected="true">in the query only</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	82 <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	83 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	84 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	85 </macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	86 <requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	87 <requirement type="package" version="2.0.0">intarna</requirement>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	88 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	89 <stdio>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	92 </stdio>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	93 <version_command>IntaRNA --version</version_command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	94 <command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	95 <![CDATA[
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	96 IntaRNA
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	97 #if $advancedOptions.advancedSelector == "advanced"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	98 ## Query parameters
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	99 --query '$advancedOptions.query._query'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	100 --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	101 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	102 --qAccFile '$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	103 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	104 --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	105 --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	106 ## #if $advancedOptions.query.qAccConstr <> "."
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	107 ## --qAccConstr $advancedOptions.query.qAccConstr
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	108 ## #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	109 --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	110 #if $advancedOptions.query.qRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	111 --qRegion '$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	112 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	113
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	114 ## Target param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	115 --target '$advancedOptions.target._target'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	116 --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	117 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	118 --tAccFile '$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	119 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	120 --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	121 --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	122 ## #if $advancedOptions.target.tAccConstr <> "."
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	123 ## --tAccConstr $advancedOptions.target.tAccConstr
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	124 ## #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	125 --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	126 #if $advancedOptions.target.tRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	127 --tRegion '$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	128 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	129
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	130 ## Seed param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	131 --noSeed $advancedOptions.seed.noSeed
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	132 --seedBP $advancedOptions.seed.seedBP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	133 --seedMaxUP $advancedOptions.seed.seedMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	134 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	135 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	136 --seedMaxE $advancedOptions.seed.seedMaxE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	137 --seedMinPu $advancedOptions.seed.seedMinPu
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	138 --seedQRange '$advancedOptions.seed.seedQRange'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	139 --seedTRange '$advancedOptions.seed.seedTRange'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	140
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	141 ## Interaction param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	142 --mode $advancedOptions.interaction.mode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	143 --pred $advancedOptions.interaction.pred
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	144 --energy $advancedOptions.interaction.energy
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	145 #if $advancedOptions.interaction.energyVRNA
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	146 --energyVRNA '$advancedOptions.interaction.energyVRNA'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	147 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	148 --temperature $advancedOptions.interaction.temperature
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	149
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	150 ##Output param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	151 --out ./temp_tabular_output
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	152 --outMode $advancedOptions.output.outMode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	153 --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	154 --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	155 --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	156 --outDeltaE $advancedOptions.output.outDeltaE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	157 #if $advancedOptions.output.outCsvCols
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	158 --outCsvCols '$advancedOptions.output.outCsvCols'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	159 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	160 #if $advancedOptions.output.add_output_cond.selector == "add"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	162 #for j in $advancedOptions.output.add_output_cond.add_output.value:
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	163 --$j $getVar($j)
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	164 #end for
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	165 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	166 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	167
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	168 #elif $advancedOptions.advancedSelector == "basic"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	169 ## Query parameters
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	170 --query '$advancedOptions.query._query'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	171 --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	172 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	173 --qAccFile '$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	174 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	175 --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	176 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	177
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	178 ## Target param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	179 --target '$advancedOptions.target._target'
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
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	187 ## Seed param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	188 --noSeed $advancedOptions.seed.noSeed
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	189 --seedBP $advancedOptions.seed.seedBP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	190 --seedMaxUP $advancedOptions.seed.seedMaxUP
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	191
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	192 ## Interaction param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	193 --mode $advancedOptions.interaction.mode
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	194
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	195 ##Output param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	196 --out ./temp_tabular_output
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	197 --outMode $advancedOptions.output.outMode
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
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	200 #if $advancedOptions.output.outCsvCols
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	201 --outCsvCols '$advancedOptions.output.outCsvCols'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	202 #end if
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
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	204 && sed 's/\t/ /g' ./temp_tabular_output > ./temp_output_no_tabs
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	205 && sed 's/;/\t/g' ./temp_output_no_tabs > '$outfile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	206
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	207 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	208 </command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	209 <inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	210
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	211 <conditional name="advancedOptions">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	212 <param name="advancedSelector" type="select" label="Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	213 <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	214 <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	215 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	216 <when value="advanced">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	217 <section name="query" title="Query Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	218 <expand macro="query_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	219 <!--
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	220 <param name="qAccConstr" type="select" label="Structure constraint for each sequence position" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	221 <option value="." selected="true">No constraint</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	222 <option value="x">Unpaired</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	223 <option value="b">Blocked positions are excluded from interaction prediction and considered unpaired </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	224 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	225 -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	226 <param argument="--qIntLoopMax" type="integer" value="16" min="0" max="30"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	227 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	228 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	229 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	230 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	231 <section name="target" title="Target Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	232 <expand macro="target_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	233 <!-- <param name="tAccConstr" type="select" label="Structure constraint for each sequence position" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	234 <option value="." selected="true">No constraint</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	235 <option value="x">Unpaired</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	236 <option value="b">Blocked.blocked positions are excluded from interaction prediction and considered unpaired </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	237 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	238 -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	239
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	240 <param argument="--tIntLoopMax" type="integer" value="16" min="0" max="30"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	241 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	242 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	243 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	244 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	245 <section name="seed" title="Seed Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	246 <expand macro="seed_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	247 <param argument="--seedQMaxUP" type="integer" value="-1" min="-1" max="20"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	248 label="Max. number of unpaired bases within the query's seed region" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	249 <param argument="--seedTMaxUP" type="integer" value="-1" min="-1" max="20"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	250 label="Max. number of unpaired bases within the target's seed region" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	251 <param argument="--seedMaxE" type="integer" value="0" min="-999" max="999"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	252 label="Max. energy a seed region may have" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	253 <param argument="--seedMinPu" type="float" value="0" min="0" max="1"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	254 label="Min. unpaired probability (per sequence)" help=""/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	255
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	256 <param argument="--seedQRange" type="text" value=""
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	257 label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	258 <param argument="--seedTRange" type="text" value=""
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	259 label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	260 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	261 <section name="interaction" title="Interaction Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	262 <expand macro="interaction_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	263 <param argument="--pred" type="select" label="Prediction target" help="Sets what to optimize for">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	264 <option value="S" selected="true">Single-site minimum-free-energy interaction</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	265 <option value="P">Single-site maximum-probability interaction</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	266 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	267 <param argument="--energy" type="select" label="Energy computation" help="">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	268 <!-- <option value="B">Base pair == -1 ()</option> -->
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	269 <option value="V" selected="true">VRNA-based computation</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	270 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	271 <param argument="--energyVRNA" type="data" format="*" optional="true"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	272 label="Energy parameter file of VRNA package" help="If not provided, the default parameter set of the linked Vienna RNA package is used."/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	273 <param argument="--temperature" type="integer" value="37" min="0" max="100"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	274 label="Temperature [°C]" help="VRNA energy parameters"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	275 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	276 <section name="output" title="Output Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	277 <expand macro="output_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	278 <param argument="--outMaxE" type="float" value="0"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	279 label="Max. absolute energy of an interaction" help="Only interactions with E ≤ maxE are reported"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	280 <param argument="--outDeltaE" type="float" value="100"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	281 label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	282
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	283 <conditional name="add_output_cond">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	284 <param name="selector" type="select" label="Additional output files">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	285 <option value="add">Output additional files</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	286 <option value="none" selected="true">Don't output additional files</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	287 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	288 <when value="add">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	289 <param name="add_output" type="select" display="checkboxes" multiple="True"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	290 label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output.">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	291 <option value="outQAccFile" selected="true">The query's ED values (--outQAccFile)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	292 <option value="outTAccFile">The target's ED values (--outTAccFile) </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	293 <option value="outQPuFile">The query's unpaired probabilities used for ED values (--outQPuFile) </option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	294 <option value="outTPuFile">The target's unpaired probabilities used for ED values (--outTPuFile)</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	295 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	296 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	297 <when value="none"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	298 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	299
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	300 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	301 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	302 <when value="basic">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	303 <section name="query" title="Query Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	304 <expand macro="query_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	305 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	306 <section name="target" title="Target Parameters" expanded="True">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	307 <expand macro="target_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	308 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	309 <section name="seed" title="Seed Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	310 <expand macro="seed_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	311 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	312 <section name="interaction" title="Interaction Parameters">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	313 <expand macro="interaction_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	314 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	315 <section name="output" title="Output Options">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	316 <expand macro="output_macro"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	317 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	318 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	319 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	320 </inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	321 <outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	322 <data name="outfile" format="text" label="IntaRNA on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	323 <change_format>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	324 <when input="advancedOptions.output.outMode" value="C" format="tabular" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	325 </change_format>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	326 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	327 <data name="outQAccFile" format="text" label="Query's ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	328 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	329 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	330 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	331 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	332 'outQAccFile' in advancedOptions['output']['add_output_cond']['add_output']
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	333 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	334 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	335 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	336 <data name="outTAccFile" format="text" label="Target's ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	337 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	338 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	339 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	340 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	341 'outTAccFile' in advancedOptions['output']['add_output_cond']['add_output']
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	342 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	343 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	344 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	345 <data name="outQPuFile" format="text" label="Query's unpaired probabilities used for ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	346 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	347 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	348 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	349 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	350 'outQPuFile' in advancedOptions['output']['add_output_cond']['add_output']
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 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	353 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	354 <data name="outTPuFile" format="text" label="Target's unpaired probabilities used for ED values, on ${on_string}">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	355 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	356 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	357 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	358 advancedOptions['output']['add_output_cond']['selector'] == "add" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	359 'outTPuFile' in advancedOptions['output']['add_output_cond']['add_output']
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	360 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	361 </filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	362 </data>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	363 </outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	364 <tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	365 <test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	366 <conditional name="advancedOptions">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	367 <param name="advancedSelector" value="basic"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	368 <section name="query">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	369 <param name="_query" value="intarna_query.fa" />
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	370 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	371 <section name="target">
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	372 <param name="_target" value="intarna_target.fa"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	373 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	374 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	375 <output name="outfile" file="intarna_result.tabular"/>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	376 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	377 </tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	378
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	379 <help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	380 <![CDATA[
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	381
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	382 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	383
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	384 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	385
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	386 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	387
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	388 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	389
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	390 .. class:: infomark
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 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	393
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	394
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	395 Input
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	396
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	397
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	398
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	399 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	400
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	401
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	402 Output
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	403
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	404 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	405
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	406 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	407
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	408 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	409
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	410 <citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	411 <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	412 <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	413 </citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	414
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	415 </tool>

0

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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1 <tool id="intarna" name="IntaRNA" version="2.0.0">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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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

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diff changeset

3 <macros>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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diff changeset

4 <macro name="query_macro">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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5 <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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6 <conditional name="qAcc_cond">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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7 <param argument="--qAcc" type="select" label="Accessibility computation" help="">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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8 <option value="N">No accessibility contributions ('N')</option>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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9 <option value="C" selected="true">Computation of accessibilities ('C')</option>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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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

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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

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diff changeset

12 </param>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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diff changeset

13 <when value="N"/>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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diff changeset

14 <when value="C"/>

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">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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16 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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diff changeset

17 </when>

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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diff changeset

18 <when value="E">

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

rnateam

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19 <param argument="--qAccFile" format="text" type="data" label="Accessibility computation" help="" />

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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20 </when>

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21 </conditional>

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22 <param argument="--qAccW" type="integer" value="150" min="0" max="99999"

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23 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>

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24 <param argument="--qAccL" type="integer" value="100" min="0" max="99999"

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25 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'"/>

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26 </macro>

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27 <macro name="target_macro">

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28 <param name="_target" argument="--target" format="fasta" type="data" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />

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29 <conditional name="tAcc_cond">

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30 <param argument="--tAcc" type="select" label="Accessibility computation" help="">

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31 <option value="N">No accessibility contributions ('N')</option>

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32 <option value="C" selected="true">Computation of accessibilities ('C')</option>

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33 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>

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34 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>

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35 </param>

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36 <when value="N"/>

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37 <when value="C"/>

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38 <when value="P">

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39 <param argument="--tAccFile" format="text" type="data" label="The file to be parsed" help="... for accessibility computation" />

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40 </when>

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41 <when value="E">

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42 <param argument="--tAccFile" format="text" type="data" label="Accessibility computation" help="" />

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43 </when>

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44 </conditional>

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45 <param argument="--tAccW" type="integer" value="150" min="0" max="99999"

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46 label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>

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47 <param argument="--tAccL" type="integer" value="100" min="0" max="99999"

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48 label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>

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49 </macro>

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50 <macro name="seed_macro">

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51 <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean"

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52 label="Disable seed constraint entirely for computation" help=""/>

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53 <param argument="--seedBP" type="integer" value="7" min="2" max="20" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>

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54 <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"

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55 label="Max. overall number of unpaired bases (query+target)" help=""/>

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56 </macro>

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57 <macro name="interaction_macro">

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58 <param argument="--mode" type="select" label="Prediction mode" help="">

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59 <option value="H" selected="true">Heuristic (fast and low memory)</option>

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60 <option value="M">Exact and low memory</option>

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61 <option value="E">Exact (high memory)</option>

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62 </param>

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63 </macro>

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64 <macro name="output_macro">

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65 <param argument="--outMode" type="select" label="Output Mode" help="">

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66 <option value="N">Normal output (ASCII char + energy)</option>

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67 <option value="D">Detailed output (ASCII char + energy/position details)</option>

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68 <option value="C" selected="true">CSV output (see --outCsvCols)</option>

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69 <option value="1">backward compatible IntaRNA v1.* normal output</option>

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70 <option value="O">backward compatible IntaRNA v1.* detailed output</option>

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71 </param>

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72

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73

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74 <param argument="--outCsvCols" type="text" optional="true"

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75 label="Comma separated list of CSV column IDs to print" 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], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2]"/>

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76 <param argument="--outNumber" type="integer" value="1" min="0" max="1000"

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77 label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/>

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78 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap">

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79 <option value="N" >in none of the sequences</option>

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80 <option value="T">in the target only</option>

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81 <option value="Q" selected="true">in the query only</option>

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82 <option value="B">in both sequences</option>

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83 </param>

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84 </macro>

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85 </macros>

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86 <requirements>

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87 <requirement type="package" version="2.0.0">intarna</requirement>

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88 </requirements>

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89 <stdio>

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90 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />

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91 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />

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92 </stdio>

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93 <version_command>IntaRNA --version</version_command>

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94 <command>

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95 <![CDATA[

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96 IntaRNA

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97 #if $advancedOptions.advancedSelector == "advanced"

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98 ## Query parameters

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99 --query '$advancedOptions.query._query'

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100 --qAcc $advancedOptions.query.qAcc_cond.qAcc

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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101 #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

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102 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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103 #end if

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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104 --qAccW $advancedOptions.query.qAccW

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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105 --qAccL $advancedOptions.query.qAccL

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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106 ## #if $advancedOptions.query.qAccConstr <> "."

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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107 ## --qAccConstr $advancedOptions.query.qAccConstr

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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108 ## #end if

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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109 --qIntLoopMax $advancedOptions.query.qIntLoopMax

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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110 #if $advancedOptions.query.qRegion

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111 --qRegion '$advancedOptions.query.qRegion'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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112 #end if

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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113

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114 ## Target param.

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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115 --target '$advancedOptions.target._target'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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116 --tAcc $advancedOptions.target.tAcc_cond.tAcc

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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117 #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

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118 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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119 #end if

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120 --tAccW $advancedOptions.target.tAccW

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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121 --tAccL $advancedOptions.target.tAccL

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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122 ## #if $advancedOptions.target.tAccConstr <> "."

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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123 ## --tAccConstr $advancedOptions.target.tAccConstr

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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124 ## #end if

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125 --tIntLoopMax $advancedOptions.target.tIntLoopMax

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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126 #if $advancedOptions.target.tRegion

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127 --tRegion '$advancedOptions.target.tRegion'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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128 #end if

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129

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130 ## Seed param.

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131 --noSeed $advancedOptions.seed.noSeed

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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132 --seedBP $advancedOptions.seed.seedBP

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133 --seedMaxUP $advancedOptions.seed.seedMaxUP

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134 --seedQMaxUP $advancedOptions.seed.seedQMaxUP

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135 --seedTMaxUP $advancedOptions.seed.seedTMaxUP

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136 --seedMaxE $advancedOptions.seed.seedMaxE

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137 --seedMinPu $advancedOptions.seed.seedMinPu

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138 --seedQRange '$advancedOptions.seed.seedQRange'

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139 --seedTRange '$advancedOptions.seed.seedTRange'

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140

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141 ## Interaction param.

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142 --mode $advancedOptions.interaction.mode

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143 --pred $advancedOptions.interaction.pred

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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144 --energy $advancedOptions.interaction.energy

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145 #if $advancedOptions.interaction.energyVRNA

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146 --energyVRNA '$advancedOptions.interaction.energyVRNA'

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147 #end if

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148 --temperature $advancedOptions.interaction.temperature

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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149

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150 ##Output param.

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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151 --out ./temp_tabular_output

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152 --outMode $advancedOptions.output.outMode

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153 --outNumber $advancedOptions.output.outNumber

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154 --outOverlap $advancedOptions.output.outOverlap

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155 --outMaxE $advancedOptions.output.outMaxE

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156 --outDeltaE $advancedOptions.output.outDeltaE

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157 #if $advancedOptions.output.outCsvCols

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158 --outCsvCols '$advancedOptions.output.outCsvCols'

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159 #end if

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160 #if $advancedOptions.output.add_output_cond.selector == "add"

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161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'

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162 #for j in $advancedOptions.output.add_output_cond.add_output.value:

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163 --$j $getVar($j)

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164 #end for

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165 #end if

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166 #end if

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167

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168 #elif $advancedOptions.advancedSelector == "basic"

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169 ## Query parameters

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170 --query '$advancedOptions.query._query'

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171 --qAcc $advancedOptions.query.qAcc_cond.qAcc

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172 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"

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173 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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174 #end if

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175 --qAccW $advancedOptions.query.qAccW

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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176 --qAccL $advancedOptions.query.qAccL

33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25

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177

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178 ## Target param.

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179 --target '$advancedOptions.target._target'

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180 --tAcc $advancedOptions.target.tAcc_cond.tAcc

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181 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"

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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

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183 #end if

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184 --tAccW $advancedOptions.target.tAccW

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185 --tAccL $advancedOptions.target.tAccL

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186

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187 ## Seed param.

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188 --noSeed $advancedOptions.seed.noSeed

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189 --seedBP $advancedOptions.seed.seedBP

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190 --seedMaxUP $advancedOptions.seed.seedMaxUP

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191

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192 ## Interaction param.

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193 --mode $advancedOptions.interaction.mode

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194

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195 ##Output param.

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196 --out ./temp_tabular_output

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197 --outMode $advancedOptions.output.outMode

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198 --outNumber $advancedOptions.output.outNumber

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199 --outOverlap $advancedOptions.output.outOverlap

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200 #if $advancedOptions.output.outCsvCols

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201 --outCsvCols '$advancedOptions.output.outCsvCols'

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202 #end if

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203 #end if

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204 && sed 's/\t/ /g' ./temp_tabular_output > ./temp_output_no_tabs

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205 && sed 's/;/\t/g' ./temp_output_no_tabs > '$outfile'

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206

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207 ]]>

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208 </command>

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209 <inputs>

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210

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211 <conditional name="advancedOptions">

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212 <param name="advancedSelector" type="select" label="Options">

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213 <option value="basic">Basic Options</option>

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214 <option value="advanced">Advanced Options</option>

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215 </param>

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216 <when value="advanced">

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217 <section name="query" title="Query Parameters" expanded="True">

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218 <expand macro="query_macro"/>

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219 <!--

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220 <param name="qAccConstr" type="select" label="Structure constraint for each sequence position" help="">

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221 <option value="." selected="true">No constraint</option>

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222 <option value="x">Unpaired</option>

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223 <option value="b">Blocked positions are excluded from interaction prediction and considered unpaired </option>

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224 </param>

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225 -->

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226 <param argument="--qIntLoopMax" type="integer" value="16" min="0" max="30"

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227 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/>

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228 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction"

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229 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />

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230 </section>

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231 <section name="target" title="Target Parameters" expanded="True">

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232 <expand macro="target_macro"/>

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233 <!-- <param name="tAccConstr" type="select" label="Structure constraint for each sequence position" help="">

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234 <option value="." selected="true">No constraint</option>

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235 <option value="x">Unpaired</option>

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236 <option value="b">Blocked.blocked positions are excluded from interaction prediction and considered unpaired </option>

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237 </param>

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238 -->

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239

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240 <param argument="--tIntLoopMax" type="integer" value="16" min="0" max="30"

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241 label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/>

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242 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction"

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243 help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" />

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244 </section>

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245 <section name="seed" title="Seed Parameters">

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246 <expand macro="seed_macro"/>

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247 <param argument="--seedQMaxUP" type="integer" value="-1" min="-1" max="20"

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248 label="Max. number of unpaired bases within the query's seed region" help=""/>

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249 <param argument="--seedTMaxUP" type="integer" value="-1" min="-1" max="20"

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250 label="Max. number of unpaired bases within the target's seed region" help=""/>

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251 <param argument="--seedMaxE" type="integer" value="0" min="-999" max="999"

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252 label="Max. energy a seed region may have" help=""/>

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253 <param argument="--seedMinPu" type="float" value="0" min="0" max="1"

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254 label="Min. unpaired probability (per sequence)" help=""/>

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255

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256 <param argument="--seedQRange" type="text" value=""

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257 label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>

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258 <param argument="--seedTRange" type="text" value=""

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259 label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/>

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260 </section>

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261 <section name="interaction" title="Interaction Parameters">

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262 <expand macro="interaction_macro"/>

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263 <param argument="--pred" type="select" label="Prediction target" help="Sets what to optimize for">

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264 <option value="S" selected="true">Single-site minimum-free-energy interaction</option>

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265 <option value="P">Single-site maximum-probability interaction</option>

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266 </param>

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267 <param argument="--energy" type="select" label="Energy computation" help="">

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268

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269 <option value="V" selected="true">VRNA-based computation</option>

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270 </param>

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271 <param argument="--energyVRNA" type="data" format="*" optional="true"

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272 label="Energy parameter file of VRNA package" help="If not provided, the default parameter set of the linked Vienna RNA package is used."/>

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273 <param argument="--temperature" type="integer" value="37" min="0" max="100"

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274 label="Temperature [°C]" help="VRNA energy parameters"/>

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275 </section>

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276 <section name="output" title="Output Options">

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277 <expand macro="output_macro"/>

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278 <param argument="--outMaxE" type="float" value="0"

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279 label="Max. absolute energy of an interaction" help="Only interactions with E ≤ maxE are reported"/>

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280 <param argument="--outDeltaE" type="float" value="100"

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281 label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported"/>

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282

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283 <conditional name="add_output_cond">

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284 <param name="selector" type="select" label="Additional output files">

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285 <option value="add">Output additional files</option>

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286 <option value="none" selected="true">Don't output additional files</option>

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287 </param>

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288 <when value="add">

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289 <param name="add_output" type="select" display="checkboxes" multiple="True"

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290 label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output.">

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291 <option value="outQAccFile" selected="true">The query's ED values (--outQAccFile)</option>

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292 <option value="outTAccFile">The target's ED values (--outTAccFile) </option>

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293 <option value="outQPuFile">The query's unpaired probabilities used for ED values (--outQPuFile) </option>

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294 <option value="outTPuFile">The target's unpaired probabilities used for ED values (--outTPuFile)</option>

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295 </param>

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296 </when>

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297 <when value="none"/>

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298 </conditional>

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299

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300 </section>

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301 </when>

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302 <when value="basic">

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303 <section name="query" title="Query Parameters" expanded="True">

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304 <expand macro="query_macro"/>

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305 </section>

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306 <section name="target" title="Target Parameters" expanded="True">

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307 <expand macro="target_macro"/>

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308 </section>

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309 <section name="seed" title="Seed Parameters">

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310 <expand macro="seed_macro"/>

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311 </section>

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312 <section name="interaction" title="Interaction Parameters">

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313 <expand macro="interaction_macro"/>

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314 </section>

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315 <section name="output" title="Output Options">

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316 <expand macro="output_macro"/>

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317 </section>

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318 </when>

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319 </conditional>

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320 </inputs>

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321 <outputs>

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322 <data name="outfile" format="text" label="IntaRNA on ${on_string}">

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323 <change_format>

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324 <when input="advancedOptions.output.outMode" value="C" format="tabular" />

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325 </change_format>

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326 </data>

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327 <data name="outQAccFile" format="text" label="Query's ED values, on ${on_string}">

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328 <filter>

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329 ((

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330 advancedOptions['advancedSelector'] == "advanced" and

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331 advancedOptions['output']['add_output_cond']['selector'] == "add" and

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332 'outQAccFile' in advancedOptions['output']['add_output_cond']['add_output']

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333 ))

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334 </filter>

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335 </data>

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336 <data name="outTAccFile" format="text" label="Target's ED values, on ${on_string}">

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337 <filter>

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338 ((

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339 advancedOptions['advancedSelector'] == "advanced" and

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340 advancedOptions['output']['add_output_cond']['selector'] == "add" and

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341 'outTAccFile' in advancedOptions['output']['add_output_cond']['add_output']

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342 ))

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343 </filter>

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344 </data>

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345 <data name="outQPuFile" format="text" label="Query's unpaired probabilities used for ED values, on ${on_string}">

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346 <filter>

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347 ((

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348 advancedOptions['advancedSelector'] == "advanced" and

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349 advancedOptions['output']['add_output_cond']['selector'] == "add" and

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350 'outQPuFile' in advancedOptions['output']['add_output_cond']['add_output']

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351 ))

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352 </filter>

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353 </data>

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354 <data name="outTPuFile" format="text" label="Target's unpaired probabilities used for ED values, on ${on_string}">

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355 <filter>

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356 ((

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357 advancedOptions['advancedSelector'] == "advanced" and

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358 advancedOptions['output']['add_output_cond']['selector'] == "add" and

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359 'outTPuFile' in advancedOptions['output']['add_output_cond']['add_output']

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360 ))

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361 </filter>

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362 </data>

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363 </outputs>

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364 <tests>

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365 <test>

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366 <conditional name="advancedOptions">

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367 <param name="advancedSelector" value="basic"/>

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368 <section name="query">

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369 <param name="_query" value="intarna_query.fa" />

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370 </section>

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371 <section name="target">

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372 <param name="_target" value="intarna_target.fa"/>

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373 </section>

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374 </conditional>

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375 <output name="outfile" file="intarna_result.tabular"/>

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376 </test>

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377 </tests>

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378

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379 <help>

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380 <![CDATA[

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381

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382 **What it does**

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383

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384 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites

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385

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386 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.

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387

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388 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.

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389

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390 .. class:: infomark

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391

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392 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.

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393

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394

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395 **Input**

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396

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397

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398

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399 RNA sequences in *FASTA* format

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400

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401

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402 **Output**

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403

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404 RNA-RNA interaction information in CSV format and additional information/files on demand

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405

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406 ]]>

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407

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408 </help>

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409

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410 <citations>

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411 <citation type="doi">10.1093/nar/gku359</citation>

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412 <citation type="doi">10.1093/bioinformatics/btn544</citation>

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413 </citations>

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414

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415 </tool>

Mercurial > repos > rnateam > intarna

annotate intarna.xml @ 0:33c0836ea386 draft