annotate intarna.xml @ 10:a3d8b6b2ffd8 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit edb936067775687e37112883c82ccda147fcb7ca"
author bgruening
date Mon, 04 Nov 2019 12:36:06 -0500
parents 56f1cef52e96
children 6e910434d5bf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
a3d8b6b2ffd8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit edb936067775687e37112883c82ccda147fcb7ca"
bgruening
parents: 9
diff changeset
1 <tool id="intarna" name="IntaRNA" version="3.1.3">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
3 <macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
4 <macro name="query_macro">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
5 <param argument="--query" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Query sequence(s)" name="query" type="data" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
6 <conditional name="qAcc_cond">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
8 <option value="N">No accessibility contributions ('N')</option>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
12 </param>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
13 <when value="N" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
14 <when value="C" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
15 <when value="P">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
16 <param argument="--qAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
17 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
18 <when value="E">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
19 <param argument="--qAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
20 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
21 </conditional>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
22 <param argument="--qAccW" help="... for query accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
23 <param argument="--qAccL" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
24 </macro>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
25 <macro name="target_macro">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
26 <param argument="--target" format="fasta" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" label="Target sequence(s)" name="target" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
27 <conditional name="tAcc_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
29 <option value="N">No accessibility contributions ('N')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
30 <option selected="true" value="C">Computation of accessibilities ('C')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
33 </param>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
34 <when value="N" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
35 <when value="C" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
36 <when value="P">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
37 <param argument="--tAccFile" format="txt" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA" label="RNAplfold unpaired probability data" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
38 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
39 <when value="E">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
40 <param argument="--tAccFile" format="txt" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA" label="IntaRNA accessibility energy penalties (ED terms)" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
41 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
42 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
43 <param argument="--tAccW" help="... for target accessibility computation. Set to 0 to use full sequence length" label="Max. interaction length" max="99999" min="0" type="integer" value="150" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
44 <param argument="--tAccL" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW'" label="Max. loop length" max="99999" min="0" type="integer" value="100" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
45 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
46 <macro name="seed_macro">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
47 <param argument="--noSeed" checked="false" falsevalue="" help="" label="Disable seed constraint entirely for computation" truevalue="--noSeed" type="boolean" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
48 <param argument="--seedBP" help="number of inter-molecular base pairs within the seed region" label="Min. number of basepairs in seed" max="20" min="2" type="integer" value="7" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
49 <param argument="--seedMaxUP" help="Maximal number of unpaired seed bases both in query and target" label="Max. overall number of unpaired bases in seed" max="10" min="0" type="integer" value="0" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
50 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
51 <macro name="interaction_macro">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
52 <param argument="--mode" help="" label="Prediction mode" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
53 <option selected="true" value="H">Heuristic ('H')</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
54 <option value="M">Exact but slow ('M')</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
55 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
56 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
57 <macro name="output_macro">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
58 <param argument="--outCsvCols" help="An empty argument prints all possible columns from the following available ID list: [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [hybridDPfull], [hybridDBfull], [E], [ED1], [ED2], [Pu1], [Pu2], [E_init], [E_loops], [E_dangleL], [E_dangleR], [E_endL], [E_endR], [E_hybrid], [E_norm], [E_hybridNorm], [E_add], [seedStart1], [seedEnd1], [seedStart2], [seedEnd2], [seedE], [seedED1], [seedED2], [seedPu1], [seedPu2], [w], [Eall], [Zall], [P_E]" label="Comma separated list of CSV column IDs to print" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
59 <param argument="--outCsvSort" help="One of the column IDs to be printed that is used to sort the CSV table output" label="Sort CSV output for the given column label from CSV column IDs to print" type="text" value="E" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
60 <param argument="--outNumber" help="Number of optimal and suboptimal interaction to predict per query-target pair" label="Max. number of predictions per query/target pair" max="1000" min="0" type="integer" value="1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
61 <param argument="--outOverlap" help="Whether or not interactions can overlap" label="Overlapping of suboptimal predictions" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
62 <option value="N">in none of the sequences</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
63 <option value="T">in the target only</option>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
64 <option selected="true" value="Q">in the query only</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
65 <option value="B">in both sequences</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
66 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
67 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
68 </macros>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
69 <requirements>
10
a3d8b6b2ffd8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit edb936067775687e37112883c82ccda147fcb7ca"
bgruening
parents: 9
diff changeset
70 <requirement type="package" version="3.1.3">intarna</requirement>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
71 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
72 <version_command>IntaRNA --version</version_command>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
73 <command detect_errors="exit_code"><![CDATA[
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
74
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
75 IntaRNA
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
76 ## Multithreading
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
77 --threads "\${GALAXY_SLOTS:-1}"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
78 ## basic general parameters
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
79 ## Query parameters
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
80 --query '$advancedOptions.query.query'
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
81 --qAcc $advancedOptions.query.qAcc_cond.qAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
82 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
83 --qAccFile '$advancedOptions.query.qAcc_cond.qAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
84 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
85 --qAccW $advancedOptions.query.qAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
86 --qAccL $advancedOptions.query.qAccL
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
87 ## Target param.
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
88 --target '$advancedOptions.target.target'
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
89 --tAcc $advancedOptions.target.tAcc_cond.tAcc
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
90 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E"
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
91 --tAccFile '$advancedOptions.target.tAcc_cond.tAccFile'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
92 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
93 --tAccW $advancedOptions.target.tAccW
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
94 --tAccL $advancedOptions.target.tAccL
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
95 ## Seed param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
96 #if $advancedOptions.seed.noSeed
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
97 $advancedOptions.seed.noSeed
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
98 #else
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
99 --seedBP $advancedOptions.seed.seedBP
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
100 #if $advancedOptions.seed.seedMaxUP > 0
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
101 --seedMaxUP $advancedOptions.seed.seedMaxUP
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
102 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
103 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
104 ## Prediction param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
105 --mode $advancedOptions.interaction.mode
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
106 --energy V
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
107 ## Output param.
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
108 --out $outfile
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
109 --outMode C
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
110 --outSep "`printf "\t"`"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
111 --outNumber $advancedOptions.output.outNumber
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
112 --outOverlap $advancedOptions.output.outOverlap
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
113 --outCsvCols '$advancedOptions.output.outCsvCols'
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
114 --outCsvSort '$advancedOptions.output.outCsvSort'
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
115 #if $advancedOptions.advancedSelector == "advanced"
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
116 ## Query parameters
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
117 --qIntLoopMax $advancedOptions.query.qIntLoopMax
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
118 #if $advancedOptions.query.qRegion
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
119 --qRegion '$advancedOptions.query.qRegion'
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
120 #end if
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
121 ## Target param.
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
122 --tIntLoopMax $advancedOptions.target.tIntLoopMax
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
123 #if $advancedOptions.target.tRegion
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
124 --tRegion '$advancedOptions.target.tRegion'
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
125 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
126 ## Seed param.
9
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents: 7
diff changeset
127 #if not $advancedOptions.seed.noSeed
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
128 --seedMaxE $advancedOptions.seed.seedMaxE
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
129 --seedMinPu $advancedOptions.seed.seedMinPu
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
130 #if $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
131 --seedQMaxUP $advancedOptions.seed.seedQMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
132 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
133 #if $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
134 --seedTMaxUP $advancedOptions.seed.seedTMaxUP
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
135 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
136 #if $advancedOptions.seed.seedQRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
137 --seedQRange '$advancedOptions.seed.seedQRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
138 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
139 #if $advancedOptions.seed.seedTRange
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
140 --seedTRange '$advancedOptions.seed.seedTRange'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
141 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
142 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
143 ## SHAPE param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
144 #if $advancedOptions.shape.qShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
145 --qShape '$advancedOptions.shape.qShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
146 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
147 #if $advancedOptions.shape.tShape
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
148 --tShape '$advancedOptions.shape.tShape'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
149 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
150 ## Prediction param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
151 --model $advancedOptions.interaction.model
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
152 --energyVRNA '$advancedOptions.interaction.energyVRNA'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
153 --temperature $advancedOptions.interaction.temperature
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
154 #if $advancedOptions.interaction.windowWidth
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
155 --windowWidth $advancedOptions.interaction.windowWidth
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
156 --windowOverlap $advancedOptions.interaction.windowOverlap
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
157 #end if
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
158 ##Output param.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
159 --outMaxE $advancedOptions.output.outMaxE
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
160 --outDeltaE $advancedOptions.output.outDeltaE
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
161 ## add additional output files
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
162 #if $advancedOptions.output.add_output_cond.selector == "add"
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
163 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
164 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
165 #if $outFile == 'qAcc' or $outFile == 'tAcc'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
166 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
167 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
168 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
169 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
170 #else
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
171 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
172 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
173 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
174 --out '$curOutFile'
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
175 #end for
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
176 #end if
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
177 #end if
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
178 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
179 ]]>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
180 </command>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
181 <inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
182 <conditional name="advancedOptions">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
183 <param label="Options" name="advancedSelector" type="select">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
184 <option value="basic">Basic Options</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
185 <option value="advanced">Advanced Options</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
186 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
187 <when value="advanced">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
188 <section expanded="True" name="query" title="Query Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
189 <expand macro="query_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
190 <param argument="--qIntLoopMax" help="... to be considered in interactions within the query" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
191 <param argument="--qRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Query regions to be considered for interaction prediction" optional="true" type="text" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
192 </section>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
193 <section expanded="True" name="target" title="Target Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
194 <expand macro="target_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
195 <param argument="--tIntLoopMax" help="... to be considered in interactions within the target" label="Maximal number of unpaired bases between neighbored interacting bases" max="30" min="0" type="integer" value="16" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
196 <param argument="--tRegion" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1" label="Target regions to be considered for interaction prediction" optional="true" type="text" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
197 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
198 <section name="seed" title="Seed Parameters">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
199 <expand macro="seed_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
200 <param argument="--seedQMaxUP" help="" label="Max. number of unpaired bases within the query's seed region" max="20" min="-1" type="integer" value="-1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
201 <param argument="--seedTMaxUP" help="" label="Max. number of unpaired bases within the target's seed region" max="20" min="-1" type="integer" value="-1" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
202 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
203 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
204 <param argument="--seedQRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the query to search for seeds" optional="true" type="text" value="" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
205 <param argument="--seedTRange" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)" label="Interval(s) in the target to search for seeds" optional="true" type="text" value="" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
206 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
207 <section name="shape" title="SHAPE Input Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
208 <param argument="--qShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
209 <param argument="--tShape" format="txt" help="Two column text file with sequence positions (1-based) and normalized reactivity values. Missing values may be left out, or assigned a negative score" label="SHAPE reactivity data to guide the query's accessibility computation" optional="true" type="data" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
210 </section>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
211 <section name="interaction" title="Prediction Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
212 <expand macro="interaction_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
213 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
214 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
215 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
216 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
217 </param>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
218 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
219 <option value="Turner99">Turner-1999</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
220 <option selected="true" value="Turner04">Turner-2004</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
221 <option value="Andronescu07">Andronescu-2007</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
222 </param>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
223 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
224 <param argument="--windowWidth" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA." label="Window-based computation: window width" max="99999" min="10" optional="True" type="integer" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
225 <param argument="--windowOverlap" help="If window width is set, this specifies the overlap of the windows. Note, it has to exceed the maximal interaction length of both query and target." label="Window-based computation: window overlap" max="99999" min="10" type="integer" value="150" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
226 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
227 <section name="output" title="Output Options">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
228 <expand macro="output_macro" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
229 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
230 <param argument="--outDeltaE" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported" label="Max. delta energy above mfe of an interaction" type="float" value="100" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
231 <conditional name="add_output_cond">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
232 <param label="Additional output files" name="selector" type="select">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
233 <option value="add">Output additional files</option>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
234 <option selected="true" value="none">Don't output additional files</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
235 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
236 <when value="add">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
237 <param display="checkboxes" help="Written in a format similar to RNAplfold unpaired probability output." label="Additional output files" multiple="True" name="add_output" type="select">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
238 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
239 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
240 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
241 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
242 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
243 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
244 <option value="qAcc">The query's ED values (qAcc)</option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
245 <option value="tAcc">The target's ED values (tAcc) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
246 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
247 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
248 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
249 </when>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
250 <when value="none" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
251 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
252 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
253 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
254 <when value="basic">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
255 <section expanded="True" name="query" title="Query Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
256 <expand macro="query_macro" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
257 </section>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
258 <section expanded="True" name="target" title="Target Parameters">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
259 <expand macro="target_macro" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
260 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
261 <section name="seed" title="Seed Parameters">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
262 <expand macro="seed_macro" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
263 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
264 <section name="interaction" title="Interaction Parameters">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
265 <expand macro="interaction_macro" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
266 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
267 <section name="output" title="Output Options">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
268 <expand macro="output_macro" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
269 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
270 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
271 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
272 </inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
273 <outputs>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
274 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
275 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
276 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
277 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
278 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
279 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
280 'spotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
281 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
282 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
283 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;spotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
284 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
285 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
286 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
287 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
288 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
289 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
290 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
291 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
292 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
293 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
294 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
295 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
296 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
297 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
298 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
299 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
300 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
301 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
302 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
303 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tSpotProb.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
304 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
305 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
306 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
307 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
308 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
309 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
310 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
311 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
312 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
313 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;qMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
314 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
315 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
316 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
317 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
318 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
319 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
320 'tMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
321 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
322 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
323 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;tMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
324 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
325 <collection label="For all index combinations: minimal energy of any interaction covering the index pair, on ${on_string}" name="pMinE_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
326 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
327 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
328 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
329 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
330 'pMinE' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
331 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
332 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
333 <discover_datasets format="tabular" pattern="intarna_(?P&lt;designation&gt;pMinE.*)\.tabular" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
334 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
335 <collection label="Query local accessibility penalties (ED values), on ${on_string}" name="qAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
336 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
337 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
338 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
339 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
340 'qAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
341 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
342 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
343 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
344 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
345 <collection label="Target local accessibility penalties (ED values), on ${on_string}" name="tAcc_output" type="list">
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
346 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
347 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
348 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
349 advancedOptions['output']['add_output_cond']['selector'] == "add" and
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
350 'tAcc' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
351 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
352 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
353 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tAcc.*)\.led" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
354 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
355 <collection label="Query local unpaired probabilities, on ${on_string}" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
356 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
357 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
358 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
359 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
360 'qPu' in advancedOptions['output']['add_output_cond']['add_output']
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
361 ))
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
362 </filter>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
363 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;qPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
364 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
365 <collection label="Target local unpaired probabilities, on ${on_string}" name="tPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
366 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
367 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
368 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
369 advancedOptions['output']['add_output_cond']['selector'] == "add" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
370 'tPu' in advancedOptions['output']['add_output_cond']['add_output']
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
371 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
372 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
373 <discover_datasets format="txt" pattern="intarna_(?P&lt;designation&gt;tPu.*)\.lpu" visible="true" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
374 </collection>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
375 </outputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
376 <tests>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
377 <test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
378 <conditional name="advancedOptions">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
379 <param name="advancedSelector" value="basic" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
380 <section name="query">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
381 <param name="query" value="intarna_query.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
382 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
383 <section name="target">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
384 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
385 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
386 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
387 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
388 </test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
389 <test>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
390 <conditional name="advancedOptions">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
391 <param name="advancedSelector" value="advanced" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
392 <section name="query">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
393 <param name="query" value="intarna_query.fa" />
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
394 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
395 <section name="target">
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
396 <param name="target" value="intarna_target.fa" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
397 </section>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
398 <section name="output">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
399 <conditional name="add_output_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
400 <param name="selector" value="add" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
401 <param name="add_output" value="spotProb,qMinE,tAcc,qPu" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
402 </conditional>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
403 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
404 </conditional>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
405 <output file="intarna_result.tabular" name="outfile" />
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
406 <output_collection count="4" name="spotProb_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
407 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
408 <output_collection count="4" name="qMinE_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
409 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
410 <output_collection count="2" name="qPu_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
411 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
412 <output_collection count="2" name="tAcc_output" type="list">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
413 </output_collection>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
414 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
415 </tests>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
diff changeset
416 <help><![CDATA[
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
417
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
418 **What it does**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
419 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
420 During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
421 IntaRNA, developed by `Prof. Backofen's bioinformatics group at Freiburg University <http://www.bioinf.uni-freiburg.de/>`_, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
422 .. class:: infomark
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
423 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information.
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
424 **Input**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
425 RNA sequences in *FASTA* format
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
426 **Output**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
427 RNA-RNA interaction information in CSV format and additional information/files on demand
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
428
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
429 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
430 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
431 <citations>
3
03c09b961567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d
rnateam
parents: 2
diff changeset
432 <citation type="doi">10.1093/nar/gkx279</citation>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
433 <citation type="doi">10.1093/nar/gku359</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
434 <citation type="doi">10.1093/bioinformatics/btn544</citation>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
435 </citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff changeset
436 </tool>