intarna: intarna.xml annotate

annotate intarna.xml @ 1:74ce9e99e73f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty

author	rnateam
date	Thu, 07 Sep 2017 08:47:53 -0400
parents	f1d6e85c6efe
children	9af43aef6997

rev	line source
1 74ce9e99e73f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty rnateam parents: 0 diff changeset	1 <tool id="intarna" name="IntaRNA" version="2.0.4">
0 f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	3 <macros>
f1d6e85c6efe 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">
f1d6e85c6efe 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" />
f1d6e85c6efe 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">
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	12 </param>
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"/>
f1d6e85c6efe 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">
f1d6e85c6efe 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="" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	17 </when>
f1d6e85c6efe 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">
f1d6e85c6efe 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="" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	20 </when>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	21 </conditional>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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'"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	26 </macro>
f1d6e85c6efe 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">
f1d6e85c6efe 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" />
f1d6e85c6efe 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">
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	35 </param>
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"/>
f1d6e85c6efe 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">
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	40 </when>
f1d6e85c6efe 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">
f1d6e85c6efe 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="" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	43 </when>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	44 </conditional>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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'"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	49 </macro>
f1d6e85c6efe 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">
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	56 </macro>
f1d6e85c6efe 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">
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	62 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	63 </macro>
f1d6e85c6efe 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">
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	71 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	72
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	73
f1d6e85c6efe 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"
f1d6e85c6efe 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]"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	83 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	84 </macro>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	85 </macros>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	86 <requirements>
1 74ce9e99e73f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty rnateam parents: 0 diff changeset	87 <requirement type="package" version="2.0.4">intarna</requirement>
0 f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	88 </requirements>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	89 <stdio>
f1d6e85c6efe 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" />
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	92 </stdio>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	94 <command>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	95 <![CDATA[
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	96 IntaRNA
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	97 #if $advancedOptions.advancedSelector == "advanced"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	98 ## Query parameters
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	99 --query '$advancedOptions.query._query'
f1d6e85c6efe 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
f1d6e85c6efe 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 $advancedOptions.query.qAcc_cond.qAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	102 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	103 #end if
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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 <> "."
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	108 ## #end if
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	110 #if $advancedOptions.query.qRegion
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	111 --qRegion '$advancedOptions.query.qRegion'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	112 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	113
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	114 ## Target param.
f1d6e85c6efe 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'
f1d6e85c6efe 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
f1d6e85c6efe 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 $advancedOptions.target.tAcc_cond.tAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	118 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	119 #end if
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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 <> "."
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	124 ## #end if
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	126 #if $advancedOptions.target.tRegion
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	127 --tRegion '$advancedOptions.target.tRegion'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	128 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	129
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	130 ## Seed param.
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	137 --seedMinPu $advancedOptions.seed.seedMinPu
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	138 --seedQRange '$advancedOptions.seed.seedQRange'
f1d6e85c6efe 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'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	140
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	141 ## Interaction param.
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	145 #if $advancedOptions.interaction.energyVRNA
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	146 --energyVRNA '$advancedOptions.interaction.energyVRNA'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	147 #end if
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	149
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	150 ##Output param.
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	157 #if $advancedOptions.output.outCsvCols
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	158 --outCsvCols '$advancedOptions.output.outCsvCols'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	159 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	160 #if $advancedOptions.output.add_output_cond.selector == "add"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	161 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
f1d6e85c6efe 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 $advancedOptions.output.add_output_cond.add_output.value:
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	163 --$j $getVar($j)
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	164 #end for
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	165 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	166 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	167
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	168 #elif $advancedOptions.advancedSelector == "basic"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	169 ## Query parameters
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	170 --query '$advancedOptions.query._query'
f1d6e85c6efe 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
f1d6e85c6efe 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 $advancedOptions.query.qAcc_cond.qAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	173 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	174 #end if
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	176 --qAccL $advancedOptions.query.qAccL
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	177
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	178 ## Target param.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	179 --target '$advancedOptions.target._target'
f1d6e85c6efe 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
f1d6e85c6efe 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 $advancedOptions.target.tAcc_cond.tAcc == "E"
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	182 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	183 #end if
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	186
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	187 ## Seed param.
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	191
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	192 ## Interaction param.
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	194
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	195 ##Output param.
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	200 #if $advancedOptions.output.outCsvCols
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	201 --outCsvCols '$advancedOptions.output.outCsvCols'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	202 #end if
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	203 #end if
f1d6e85c6efe 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
f1d6e85c6efe 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'
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	206
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	207 ]]>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	208 </command>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	209 <inputs>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	210
f1d6e85c6efe 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">
f1d6e85c6efe 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">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	215 </param>
f1d6e85c6efe 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">
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	219 <!--
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	224 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	225 -->
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	230 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe 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="">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	237 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	238 -->
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	239
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	244 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe 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"
f1d6e85c6efe 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=""/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	255
f1d6e85c6efe 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=""
f1d6e85c6efe 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)"/>
f1d6e85c6efe 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=""
f1d6e85c6efe 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)"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	260 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe 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">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	266 </param>
f1d6e85c6efe 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="">
f1d6e85c6efe 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> -->
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	270 </param>
1 74ce9e99e73f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 8f81e944ec7edd1777f0eb679b8a425e4f58b69e-dirty rnateam parents: 0 diff changeset	271 <param argument="--energyVRNA" type="data" format="txt" optional="true"
0 f1d6e85c6efe 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."/>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	275 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe 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"
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	282
f1d6e85c6efe 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">
f1d6e85c6efe 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">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	287 </param>
f1d6e85c6efe 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">
f1d6e85c6efe 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"
f1d6e85c6efe 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.">
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	295 </param>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	296 </when>
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	298 </conditional>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	299
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	300 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	301 </when>
f1d6e85c6efe 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">
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	305 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	308 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	311 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	314 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	317 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	318 </when>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	319 </conditional>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	320 </inputs>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	321 <outputs>
f1d6e85c6efe 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}">
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	323 <change_format>
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	325 </change_format>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	326 </data>
f1d6e85c6efe 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}">
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	328 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	329 ((
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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']
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	333 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	334 </filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	335 </data>
f1d6e85c6efe 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}">
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	337 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	338 ((
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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']
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	342 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	343 </filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	344 </data>
f1d6e85c6efe 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}">
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	346 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	347 ((
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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']
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	351 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	352 </filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	353 </data>
f1d6e85c6efe 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}">
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	355 <filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	356 ((
f1d6e85c6efe 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
f1d6e85c6efe 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
f1d6e85c6efe 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']
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	360 ))
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	361 </filter>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	362 </data>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	363 </outputs>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	364 <tests>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	365 <test>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe 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">
f1d6e85c6efe 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" />
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	370 </section>
f1d6e85c6efe 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">
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	373 </section>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	374 </conditional>
f1d6e85c6efe 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"/>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	376 </test>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	377 </tests>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	378
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	379 <help>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	380 <![CDATA[
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	381
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	383
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	385
f1d6e85c6efe 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.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	387
f1d6e85c6efe 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.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	389
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	390 .. class:: infomark
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	391
f1d6e85c6efe 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.
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	393
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	394
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	395 Input
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	396
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	397
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	398
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	400
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	401
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	402 Output
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	403
f1d6e85c6efe 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
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	405
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	406 ]]>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	407
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	408 </help>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	409
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	410 <citations>
f1d6e85c6efe 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>
f1d6e85c6efe 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>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	413 </citations>
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	414
f1d6e85c6efe planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25 rnateam parents: diff changeset	415 </tool>

Mercurial > repos > rnateam > intarna

annotate intarna.xml @ 1:74ce9e99e73f draft