Mercurial > repos > rnateam > intarna

annotate intarna.xml @ 10:a3d8b6b2ffd8 draft

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"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
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10
a3d8b6b2ffd8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit edb936067775687e37112883c82ccda147fcb7ca"
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1 <tool id="intarna" name="IntaRNA" version="3.1.3">
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33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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3 <macros>
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4 <macro name="query_macro">
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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" />
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6 <conditional name="qAcc_cond">
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7 <param argument="--qAcc" help="" label="Accessibility computation" type="select">
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8 <option value="N">No accessibility contributions ('N')</option>
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9 <option selected="true" value="C">Computation of accessibilities ('C')</option>
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10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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12 </param>
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13 <when value="N" />
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14 <when value="C" />
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15 <when value="P">
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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" />
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17 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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18 <when value="E">
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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" />
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20 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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21 </conditional>
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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"
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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"
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24 </macro>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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25 <macro name="target_macro">
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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"
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27 <conditional name="tAcc_cond">
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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28 <param argument="--tAcc" help="" label="Accessibility computation" type="select">
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29 <option value="N">No accessibility contributions ('N')</option>
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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"
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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"
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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"
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33 </param>
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34 <when value="N" />
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35 <when value="C" />
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36 <when value="P">
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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"
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38 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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39 <when value="E">
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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"
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41 </when>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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42 </conditional>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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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" />
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45 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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46 <macro name="seed_macro">
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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"
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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"
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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" />
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50 </macro>
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51 <macro name="interaction_macro">
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52 <param argument="--mode" help="" label="Prediction mode" type="select">
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53 <option selected="true" value="H">Heuristic ('H')</option>
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54 <option value="M">Exact but slow ('M')</option>
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55 </param>
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56 </macro>
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57 <macro name="output_macro">
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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"
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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"
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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"
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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"
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62 <option value="N">in none of the sequences</option>
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63 <option value="T">in the target only</option>
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64 <option selected="true" value="Q">in the query only</option>
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65 <option value="B">in both sequences</option>
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66 </param>
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67 </macro>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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68 </macros>
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69 <requirements>
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a3d8b6b2ffd8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit edb936067775687e37112883c82ccda147fcb7ca"
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70 <requirement type="package" version="3.1.3">intarna</requirement>
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71 </requirements>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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72 <version_command>IntaRNA --version</version_command>
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fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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
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diff changeset
108 --out $outfile
56f1cef52e96 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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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
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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
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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
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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
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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
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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
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129 --seedMinPu $advancedOptions.seed.seedMinPu
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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132 #end if
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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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
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diff changeset
143 ## SHAPE param.
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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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
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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
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158 ##Output param.
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159 --outMaxE $advancedOptions.output.outMaxE
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160 --outDeltaE $advancedOptions.output.outDeltaE
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161 ## add additional output files
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162 #if $advancedOptions.output.add_output_cond.selector == "add"
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163 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None'
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164 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value:
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165 #if $outFile == 'qAcc' or $outFile == 'tAcc'
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166 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led'
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167 #else
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168 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu'
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169 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu'
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170 #else
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171 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular'
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172 #end if
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173 #end if
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174 --out '$curOutFile'
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175 #end for
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176 #end if
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177 #end if
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178 #end if
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179 ]]>
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180 </command>
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181 <inputs>
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182 <conditional name="advancedOptions">
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183 <param label="Options" name="advancedSelector" type="select">
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184 <option value="basic">Basic Options</option>
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185 <option value="advanced">Advanced Options</option>
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186 </param>
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187 <when value="advanced">
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188 <section expanded="True" name="query" title="Query Parameters">
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189 <expand macro="query_macro" />
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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" />
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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" />
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192 </section>
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193 <section expanded="True" name="target" title="Target Parameters">
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194 <expand macro="target_macro" />
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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" />
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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" />
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197 </section>
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198 <section name="seed" title="Seed Parameters">
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199 <expand macro="seed_macro" />
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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" />
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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" />
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202 <param argument="--seedMaxE" help="" label="Max. energy a seed region may have" max="999" min="-999" type="integer" value="0" />
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203 <param argument="--seedMinPu" help="" label="Min. unpaired probability (per sequence)" max="1" min="0" type="float" value="0" />
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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="" />
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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="" />
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206 </section>
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207 <section name="shape" title="SHAPE Input Parameters">
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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" />
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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" />
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210 </section>
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211 <section name="interaction" title="Prediction Parameters">
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212 <expand macro="interaction_macro" />
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213 <param argument="--model" help="Sets what to optimize for" label="Prediction target" type="select">
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214 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option>
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215 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option>
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216 <option value="P">Single-site interaction with minimal free ensemble energy per site</option>
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217 </param>
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218 <param argument="--energyVRNA" help="" label="Energy parameter" type="select">
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219 <option value="Turner99">Turner-1999</option>
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220 <option selected="true" value="Turner04">Turner-2004</option>
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221 <option value="Andronescu07">Andronescu-2007</option>
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222 </param>
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223 <param argument="--temperature" help="Temperature scaling of ViennaRNA energy parameters" label="Temperature [Celsius]" max="100" min="0" type="integer" value="37" />
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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" />
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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" />
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226 </section>
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227 <section name="output" title="Output Options">
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228 <expand macro="output_macro" />
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229 <param argument="--outMaxE" help="Only interactions with E ≤ maxE are reported" label="Max. absolute energy of an interaction" type="float" value="0" />
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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" />
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231 <conditional name="add_output_cond">
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232 <param label="Additional output files" name="selector" type="select">
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233 <option value="add">Output additional files</option>
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234 <option selected="true" value="none">Don't output additional files</option>
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235 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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236 <when value="add">
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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247 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option>
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248 </param>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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249 </when>
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250 <when value="none" />
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251 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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252 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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253 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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254 <when value="basic">
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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"
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256 <expand macro="query_macro" />
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257 </section>
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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"
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259 <expand macro="target_macro" />
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260 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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261 <section name="seed" title="Seed Parameters">
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fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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262 <expand macro="seed_macro" />
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263 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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264 <section name="interaction" title="Interaction Parameters">
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fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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265 <expand macro="interaction_macro" />
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266 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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267 <section name="output" title="Output Options">
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268 <expand macro="output_macro" />
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269 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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270 </when>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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271 </conditional>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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272 </inputs>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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273 <outputs>
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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"
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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"
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276 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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277 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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278 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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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"
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281 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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282 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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284 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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286 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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287 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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288 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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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"
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291 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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292 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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294 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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296 <filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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297 ((
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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298 advancedOptions['advancedSelector'] == "advanced" and
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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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"
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301 ))
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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302 </filter>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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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"
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304 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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305 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list">
0
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306 <filter>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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307 ((
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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308 advancedOptions['advancedSelector'] == "advanced" and
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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309 advancedOptions['output']['add_output_cond']['selector'] == "add" and
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310 'qMinE' in advancedOptions['output']['add_output_cond']['add_output']
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33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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311 ))
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312 </filter>
7
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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"
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314 </collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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315 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list">
0
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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
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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
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402 </conditional>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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403 </section>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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404 </conditional>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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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
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407 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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409 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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411 </output_collection>
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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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
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413 </output_collection>
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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414 </test>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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415 </tests>
7
fd067a1143f3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents: 6
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416 <help><![CDATA[
0
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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417
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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418 **What it does**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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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
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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
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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
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422 .. class:: infomark
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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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
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424 **Input**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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425 RNA sequences in *FASTA* format
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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426 **Output**
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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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
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428
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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429 ]]>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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430 </help>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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431 <citations>
3
03c09b961567 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d
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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
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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
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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
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435 </citations>
33c0836ea386 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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436 </tool>