Mercurial > repos > rnateam > intarna
annotate intarna.xml @ 16:f5d850723e63 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
| author | bgruening |
|---|---|
| date | Wed, 18 Sep 2024 19:42:08 +0000 |
| parents | 0377acb3f91b |
| children |
| rev | line source |
|---|---|
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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1 <tool id="intarna" name="IntaRNA" version="3.4.1" profile="23.0"> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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2 <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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3 <macros> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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4 <macro name="query_macro"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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5 <param argument="--query" type="data" format="fasta" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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6 <conditional name="qAcc_cond"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
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7 <param argument="--qAcc" type="select" label="Accessibility computation" help=""> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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8 <option value="N">No accessibility contributions ('N')</option> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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9 <option selected="true" value="C">Computation of accessibilities ('C')</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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10 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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11 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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12 </param> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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13 <when value="N"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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changeset
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14 <when value="C"/> |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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15 <when value="P"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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16 <param argument="--qAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/> |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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17 </when> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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18 <when value="E"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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19 <param argument="--qAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/> |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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20 </when> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
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21 </conditional> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
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22 <param argument="--qAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
changeset
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23 <param argument="--qAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'qAccW"/> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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24 </macro> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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25 <macro name="target_macro"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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26 <param argument="--target" type="data" format="fasta" label="Target sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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27 <conditional name="tAcc_cond"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
changeset
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28 <param argument="--tAcc" type="select" label="Accessibility computation" help=""> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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29 <option value="N">No accessibility contributions ('N')</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
changeset
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30 <option selected="true" value="C">Computation of accessibilities ('C')</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
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31 <option value="P">Unpaired probabilities in RNAplfold format from --qAccFile</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
changeset
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32 <option value="E">ED values in RNAplfold Pu-like format from --qAccFile</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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33 </param> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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34 <when value="N"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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35 <when value="C"/> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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36 <when value="P"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
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37 <param argument="--tAccFile" type="data" format="txt" label="RNAplfold unpaired probability data" help="Unpaired probabilities for subsequences as computed and reported by RNAplfold or IntaRNA"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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38 </when> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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39 <when value="E"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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40 <param argument="--tAccFile" type="data" format="txt" label="IntaRNA accessibility energy penalties (ED terms)" help="Accessibility energy penalty terms (ED) for subsequences as computed and reported by IntaRNA"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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41 </when> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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42 </conditional> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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43 <param argument="--tAccW" type="integer" min="0" max="99999" value="150" label="Max. interaction length" help="... for target accessibility computation. Set to 0 to use full sequence length"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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44 <param argument="--tAccL" type="integer" min="0" max="99999" value="100" label="Max. loop length" help="... for target accessibility computation. 0 defaults to sliding window size 'tAccW"/> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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45 </macro> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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46 <macro name="seed_macro"> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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47 <param argument="--noSeed" type="boolean" truevalue="--noSeed" falsevalue="" checked="false" label="Disable seed constraint entirely for computation" help=""/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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48 <param argument="--seedBP" type="integer" min="2" max="20" value="7" label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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49 <param argument="--seedMaxUP" type="integer" min="0" max="10" value="0" label="Max. overall number of unpaired bases in seed" help="Maximal number of unpaired seed bases both in query and target"/> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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50 </macro> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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51 <macro name="interaction_macro"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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52 <param argument="--mode" type="select" label="Prediction mode" help=""> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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53 <option selected="true" value="H">Heuristic ('H')</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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54 <option value="M">Exact but slow ('M')</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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55 </param> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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56 </macro> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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57 <macro name="output_macro"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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58 <param argument="--outCsvCols" type="text" value="id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E" label="Comma separated list of CSV column IDs to print" help="An empty argument prints all possible columns from the following available ID list: [id1], [id2], [seq1], [seq2], [subseq1], [subseq2], [subseqDP], [subseqDB], [start1], [end1], [start2], [end2], [hybridDP], [hybridDB], [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]"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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59 <param argument="--outCsvSort" type="text" value="E" label="Sort CSV output for the given column label from CSV column IDs to print" help="One of the column IDs to be printed that is used to sort the CSV table output"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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60 <param argument="--outNumber" type="integer" min="0" max="1000" value="1" label="Max. number of predictions per query/target pair" help="Number of optimal and suboptimal interaction to predict per query-target pair"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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61 <param argument="--outOverlap" type="select" label="Overlapping of suboptimal predictions" help="Whether or not interactions can overlap"> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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62 <option value="N">in none of the sequences</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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63 <option value="T">in the target only</option> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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64 <option selected="true" value="Q">in the query only</option> |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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65 <option value="B">in both sequences</option> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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66 </param> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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67 <param argument="--outPairwise" type="boolean" truevalue="--outPairwise" falsevalue="" checked="false" label="Enables pairwise sequence processing, i.e. interactions are only computed for each corresponding query-target pair (same index) instead of all-vs-all" help=""/> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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68 </macro> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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69 </macros> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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70 <requirements> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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71 <requirement type="package" version="3.4.1">intarna</requirement> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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72 </requirements> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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73 <version_command>IntaRNA --version</version_command> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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74 <command detect_errors="exit_code"><![CDATA[ |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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|
75 |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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76 IntaRNA |
|
9
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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77 ## Multithreading |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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78 --threads "\${GALAXY_SLOTS:-1}" |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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|
79 ## basic general parameters |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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|
80 ## Query parameters |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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81 --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:
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changeset
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82 --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
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changeset
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83 #if $advancedOptions.query.qAcc_cond.qAcc == "P" or $advancedOptions.query.qAcc_cond.qAcc == "E" |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
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84 --qAccFile '$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
|
85 #end if |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
86 --qAccW $advancedOptions.query.qAccW |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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87 --qAccL $advancedOptions.query.qAccL |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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88 ## Target param. |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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89 --target '$advancedOptions.target.target' |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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changeset
|
90 --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:
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91 #if $advancedOptions.target.tAcc_cond.tAcc == "P" or $advancedOptions.target.tAcc_cond.tAcc == "E" |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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92 --tAccFile '$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
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|
93 #end if |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
94 --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
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|
95 --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:
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|
96 ## Seed param. |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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97 #if $advancedOptions.seed.noSeed |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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98 $advancedOptions.seed.noSeed |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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99 #else |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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100 --seedBP $advancedOptions.seed.seedBP |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents:
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101 #if $advancedOptions.seed.seedMaxUP > 0 |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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102 --seedMaxUP $advancedOptions.seed.seedMaxUP |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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103 #end if |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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104 #end if |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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105 ## Prediction param. |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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106 --mode $advancedOptions.interaction.mode |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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107 --energy V |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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108 ## Output param. |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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109 --out $outfile |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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110 --outMode C |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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111 --outSep "`printf "\t"`" |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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112 --outNumber $advancedOptions.output.outNumber |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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113 --outOverlap $advancedOptions.output.outOverlap |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents:
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114 --outCsvCols '$advancedOptions.output.outCsvCols' |
|
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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115 --outCsvSort '$advancedOptions.output.outCsvSort' |
|
13
ddfd02440cfa
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 76e8f82fd859dcb91b5704df4fd5d2d154ad799e"
bgruening
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116 $advancedOptions.output.outPairwise |
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9
56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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117 #if $advancedOptions.advancedSelector == "advanced" |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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118 ## Query parameters |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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119 --qIntLoopMax $advancedOptions.query.qIntLoopMax |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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120 #if $advancedOptions.query.qRegion |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
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121 --qRegion '$advancedOptions.query.qRegion' |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents:
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122 #end if |
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56f1cef52e96
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 32397c91ad9eea666d94b40b0d1992ec6b19952d"
bgruening
parents:
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123 ## Target param. |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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124 --tIntLoopMax $advancedOptions.target.tIntLoopMax |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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125 #if $advancedOptions.target.tRegion |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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126 --tRegion '$advancedOptions.target.tRegion' |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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127 #end if |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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128 ## 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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129 #if not $advancedOptions.seed.noSeed |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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130 --seedMaxE $advancedOptions.seed.seedMaxE |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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131 --seedMinPu $advancedOptions.seed.seedMinPu |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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132 #if $advancedOptions.seed.seedQMaxUP |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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133 --seedQMaxUP $advancedOptions.seed.seedQMaxUP |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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134 #end if |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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135 #if $advancedOptions.seed.seedTMaxUP |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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136 --seedTMaxUP $advancedOptions.seed.seedTMaxUP |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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137 #end if |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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138 #if $advancedOptions.seed.seedQRange |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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139 --seedQRange '$advancedOptions.seed.seedQRange' |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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140 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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141 #if $advancedOptions.seed.seedTRange |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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142 --seedTRange '$advancedOptions.seed.seedTRange' |
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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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143 #end if |
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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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144 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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145 ## SHAPE param. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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146 #if $advancedOptions.shape.qShape |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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147 --qShape '$advancedOptions.shape.qShape' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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148 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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149 #if $advancedOptions.shape.tShape |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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150 --tShape '$advancedOptions.shape.tShape' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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151 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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152 ## Prediction param. |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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153 --model $advancedOptions.interaction.model |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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154 --energyVRNA '$advancedOptions.interaction.energyVRNA' |
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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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155 --temperature $advancedOptions.interaction.temperature |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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156 #if $advancedOptions.interaction.windowWidth |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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157 --windowWidth $advancedOptions.interaction.windowWidth |
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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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158 --windowOverlap $advancedOptions.interaction.windowOverlap |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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159 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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160 ##Output param. |
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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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161 --outMaxE $advancedOptions.output.outMaxE |
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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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162 --outDeltaE $advancedOptions.output.outDeltaE |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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163 ## add additional output files |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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164 #if $advancedOptions.output.add_output_cond.selector == "add" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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165 #if str($advancedOptions.output.add_output_cond.add_output.value) != 'None' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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166 #for $outFile in $advancedOptions.output.add_output_cond.add_output.value: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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167 #if $outFile == 'qAcc' or $outFile == 'tAcc' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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168 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.led' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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169 #else |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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170 #if $outFile == 'qAcc' or $outFile == 'tAcc' or $outFile == 'qPu' or $outFile == 'tPu' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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171 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.lpu' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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172 #else |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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173 #set curOutFile = str($outFile) + ':intarna_' + str($outFile) + '.tabular' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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174 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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175 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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176 --out '$curOutFile' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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177 #end for |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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178 #end if |
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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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179 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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180 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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181 ]]> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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182 </command> |
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183 <inputs> |
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184 <conditional name="advancedOptions"> |
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185 <param name="advancedSelector" type="select" label="Options"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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186 <option value="basic">Basic Options</option> |
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187 <option value="advanced">Advanced Options</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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188 </param> |
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189 <when value="advanced"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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190 <section expanded="True" name="query" title="Query Parameters"> |
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191 <expand macro="query_macro"/> |
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192 <param argument="--qIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the query"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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193 <param argument="--qRegion" type="text" optional="true" label="Query regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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194 </section> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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195 <section expanded="True" name="target" title="Target Parameters"> |
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196 <expand macro="target_macro"/> |
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197 <param argument="--tIntLoopMax" type="integer" min="0" max="30" value="16" label="Maximal number of unpaired bases between neighbored interacting bases" help="... to be considered in interactions within the target"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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198 <param argument="--tRegion" type="text" optional="true" label="Target regions to be considered for interaction prediction" help="In the format 'from1-to1,from2-to2,..' assuming indexing starts with 1"/> |
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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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199 </section> |
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200 <section name="seed" title="Seed Parameters"> |
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201 <expand macro="seed_macro"/> |
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202 <param argument="--seedQMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the query's seed region" help=""/> |
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203 <param argument="--seedTMaxUP" type="integer" min="-1" max="20" value="-1" label="Max. number of unpaired bases within the target's seed region" help=""/> |
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204 <param argument="--seedMaxE" type="integer" min="-999" max="999" value="0" label="Max. energy a seed region may have" help=""/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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205 <param argument="--seedMinPu" type="float" min="0" max="1" value="0" label="Min. unpaired probability (per sequence)" help=""/> |
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206 <param argument="--seedQRange" type="text" value="" optional="true" label="Interval(s) in the query to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/> |
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f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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207 <param argument="--seedTRange" type="text" value="" optional="true" label="Interval(s) in the target to search for seeds" help="in format 'from1-to1,from2-to2,...' (Note, only for single query)"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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208 </section> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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209 <section name="shape" title="SHAPE Input Parameters"> |
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210 <param argument="--qShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" 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"/> |
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211 <param argument="--tShape" type="data" format="txt" optional="true" label="SHAPE reactivity data to guide the query's accessibility computation" 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"/> |
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212 </section> |
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213 <section name="interaction" title="Prediction Parameters"> |
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214 <expand macro="interaction_macro"/> |
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215 <param argument="--model" type="select" label="Prediction target" help="Sets what to optimize for"> |
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216 <option value="S">Single-site minimum-free-energy interaction (IntaRNA v1+2 mode)</option> |
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217 <option selected="true" value="X">Single-site minimum-free-energy interaction (via seed-extension)</option> |
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218 <option value="P">Single-site interaction with minimal free ensemble energy per site</option> |
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219 </param> |
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220 <param argument="--energyVRNA" type="select" label="Energy parameter" help=""> |
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221 <option value="Turner99">Turner-1999</option> |
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222 <option selected="true" value="Turner04">Turner-2004</option> |
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223 <option value="Andronescu07">Andronescu-2007</option> |
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224 </param> |
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225 <param argument="--temperature" type="integer" min="0" max="100" value="37" label="Temperature [Celsius]" help="Temperature scaling of ViennaRNA energy parameters"/> |
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226 <param argument="--windowWidth" type="integer" min="10" max="99999" optional="True" label="Window-based computation: window width" help="If set, large sequences are decomposed in overlapping windows of the given size to reduce the memory consumption of IntaRNA."/> |
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227 <param argument="--windowOverlap" type="integer" min="10" max="99999" value="150" label="Window-based computation: window overlap" 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."/> |
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228 </section> |
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229 <section name="output" title="Output Options"> |
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230 <expand macro="output_macro"/> |
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231 <param argument="--outMaxE" type="float" value="0" label="Max. absolute energy of an interaction" help="Only interactions with E ≤ maxE are reported"/> |
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232 <param argument="--outDeltaE" type="float" value="100" label="Max. delta energy above mfe of an interaction" help="suboptimal output: only interactions with E ≤ (minE+deltaE) are reported"/> |
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233 <conditional name="add_output_cond"> |
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234 <param name="selector" type="select" label="Additional output files"> |
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235 <option value="add">Output additional files</option> |
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236 <option selected="true" value="none">Don't output additional files</option> |
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237 </param> |
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238 <when value="add"> |
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239 <param name="add_output" type="select" label="Additional output files" help="Written in a format similar to RNAplfold unpaired probability output." display="checkboxes" multiple="True"> |
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240 <option value="spotProb">Spot probabilities of all index combinations (spotProb)</option> |
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241 <option value="qSpotProb">Spot probabilities for all query indices (qSpotProb)</option> |
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242 <option value="tSpotProb">Spot probabilities for all target indices (tSpotProb)</option> |
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243 <option value="pMinE">For all index combinations: minimal energy of any interaction covering the index pair (pMinE)</option> |
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244 <option value="qMinE">For all query indices: minimal energy of any interaction covering the position (qMinE)</option> |
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245 <option value="tMinE">For all target indices: minimal energy of any interaction covering the position (tMinE)</option> |
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246 <option value="qAcc">The query's ED values (qAcc)</option> |
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247 <option value="tAcc">The target's ED values (tAcc) </option> |
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248 <option value="qPu">The query's unpaired probabilities used for ED values (qPu) </option> |
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249 <option value="tPu">The target's unpaired probabilities used for ED values (tPu)</option> |
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250 </param> |
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251 </when> |
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252 <when value="none"/> |
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253 </conditional> |
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254 </section> |
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255 </when> |
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256 <when value="basic"> |
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257 <section expanded="True" name="query" title="Query Parameters"> |
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258 <expand macro="query_macro"/> |
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259 </section> |
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260 <section expanded="True" name="target" title="Target Parameters"> |
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261 <expand macro="target_macro"/> |
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262 </section> |
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263 <section name="seed" title="Seed Parameters"> |
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264 <expand macro="seed_macro"/> |
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265 </section> |
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266 <section name="interaction" title="Interaction Parameters"> |
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267 <expand macro="interaction_macro"/> |
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268 </section> |
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269 <section name="output" title="Output Options"> |
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270 <expand macro="output_macro"/> |
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271 </section> |
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272 </when> |
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273 </conditional> |
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274 </inputs> |
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275 <outputs> |
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276 <data format="tabular" label="IntaRNA on ${on_string}" name="outfile"/> |
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277 <collection label="Spot probability of all index combinations, on ${on_string}" name="spotProb_output" type="list"> |
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278 <filter> |
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279 (( |
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280 advancedOptions['advancedSelector'] == "advanced" and |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff
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|
281 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
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diff
changeset
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282 'spotProb' in advancedOptions['output']['add_output_cond']['add_output'] |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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|
283 )) |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
changeset
|
284 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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changeset
|
285 <discover_datasets format="tabular" pattern="intarna_(?P<designation>spotProb.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
286 </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
|
287 <collection label="Spot probability for all query indices, on ${on_string}" name="qSpotProb_output" type="list"> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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changeset
|
288 <filter> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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changeset
|
289 (( |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
changeset
|
290 advancedOptions['advancedSelector'] == "advanced" and |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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6
diff
changeset
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291 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
|
292 'qSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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|
293 )) |
|
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
|
294 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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295 <discover_datasets format="tabular" pattern="intarna_(?P<designation>qSpotProb.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
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|
296 </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
|
297 <collection label="Spot probability for all target indices, on ${on_string}" name="tSpotProb_output" type="list"> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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changeset
|
298 <filter> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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changeset
|
299 (( |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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changeset
|
300 advancedOptions['advancedSelector'] == "advanced" and |
|
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
|
301 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
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diff
changeset
|
302 'tSpotProb' in advancedOptions['output']['add_output_cond']['add_output'] |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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diff
changeset
|
303 )) |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
304 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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diff
changeset
|
305 <discover_datasets format="tabular" pattern="intarna_(?P<designation>tSpotProb.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
306 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
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diff
changeset
|
307 <collection label="For all query indices: minimal energy of any interaction covering the position, on ${on_string}" name="qMinE_output" type="list"> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
308 <filter> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
309 (( |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
310 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
|
311 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
|
312 'qMinE' in advancedOptions['output']['add_output_cond']['add_output'] |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
313 )) |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
314 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
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diff
changeset
|
315 <discover_datasets format="tabular" pattern="intarna_(?P<designation>qMinE.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
316 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
317 <collection label="For all target indices: minimal energy of any interaction covering the position, on ${on_string}" name="tMinE_output" type="list"> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
318 <filter> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
319 (( |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
320 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
|
321 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
|
322 '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
|
323 )) |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
324 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
15
diff
changeset
|
325 <discover_datasets format="tabular" pattern="intarna_(?P<designation>tMinE.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
326 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
327 <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
|
328 <filter> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
329 (( |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
330 advancedOptions['advancedSelector'] == "advanced" and |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
331 advancedOptions['output']['add_output_cond']['selector'] == "add" and |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
332 '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
|
333 )) |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
334 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
15
diff
changeset
|
335 <discover_datasets format="tabular" pattern="intarna_(?P<designation>pMinE.*)\.tabular" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
336 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
337 <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
|
338 <filter> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
339 (( |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
340 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
|
341 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
|
342 '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
|
343 )) |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
344 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
parents:
15
diff
changeset
|
345 <discover_datasets format="txt" pattern="intarna_(?P<designation>qAcc.*)\.led" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
346 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
parents:
6
diff
changeset
|
347 <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
|
348 <filter> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
349 (( |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
diff
changeset
|
350 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
|
351 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
|
352 '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
|
353 )) |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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354 </filter> |
|
16
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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|
355 <discover_datasets format="txt" pattern="intarna_(?P<designation>tAcc.*)\.led" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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356 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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357 <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
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358 <filter> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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359 (( |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
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360 advancedOptions['advancedSelector'] == "advanced" and |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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361 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
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362 '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
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363 )) |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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|
364 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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365 <discover_datasets format="txt" pattern="intarna_(?P<designation>qPu.*)\.lpu" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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366 </collection> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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367 <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
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368 <filter> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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369 (( |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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370 advancedOptions['advancedSelector'] == "advanced" and |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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371 advancedOptions['output']['add_output_cond']['selector'] == "add" and |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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372 '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"
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373 )) |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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374 </filter> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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375 <discover_datasets format="txt" pattern="intarna_(?P<designation>tPu.*)\.lpu" visible="true"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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376 </collection> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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377 </outputs> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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378 <tests> |
|
16
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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379 <test expect_num_outputs="1"> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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380 <conditional name="advancedOptions"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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381 <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
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382 <section name="query"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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383 <param name="query" value="intarna_query.fa"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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384 </section> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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385 <section name="target"> |
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16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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386 <param name="target" value="intarna_target.fa"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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387 </section> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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388 </conditional> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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389 <output file="intarna_result.tabular" name="outfile"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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390 </test> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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391 <test expect_num_outputs="5"> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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392 <conditional name="advancedOptions"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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393 <param name="advancedSelector" value="advanced"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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394 <section name="query"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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395 <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
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396 </section> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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397 <section name="target"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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398 <param name="target" value="intarna_target.fa"/> |
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7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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399 </section> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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400 <section name="output"> |
|
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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401 <conditional name="add_output_cond"> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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402 <param name="selector" value="add"/> |
|
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
bgruening
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403 <param name="add_output" value="spotProb,qMinE,tAcc,qPu"/> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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404 </conditional> |
|
0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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405 </section> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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406 </conditional> |
|
16
f5d850723e63
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 1b6ed16ed74f60624e7c379c991a5de0e060144c
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407 <output file="intarna_result.tabular" name="outfile"/> |
|
7
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="spotProb_output" type="list"> |
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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="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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411 </output_collection> |
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fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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412 <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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413 </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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414 <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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415 </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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416 </test> |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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417 </tests> |
|
7
fd067a1143f3
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 6529d7f585194b5a8bed7c19707dc918f18ec6fc"
bgruening
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418 <help><![CDATA[ |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
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419 |
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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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420 **What it does** |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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421 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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422 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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423 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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424 .. class:: infomark |
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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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425 Please refer to `IntaRNA github repository <https://github.com/BackofenLab/IntaRNA>`_ for use cases and additional information. |
|
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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426 **Input** |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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427 RNA sequences in *FASTA* format |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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428 **Output** |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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429 RNA-RNA interaction information in CSV format and additional information/files on demand |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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430 |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
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431 ]]> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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432 </help> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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433 <citations> |
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3
03c09b961567
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit 0d69e178bbd7019a51a50fda5e5cf6721770083d
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434 <citation type="doi">10.1093/nar/gkx279</citation> |
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0
33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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435 <citation type="doi">10.1093/nar/gku359</citation> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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436 <citation type="doi">10.1093/bioinformatics/btn544</citation> |
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33c0836ea386
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit bd39ebb8525db1e0f6a7e232bc05a5eea6badd25
rnateam
parents:
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437 </citations> |
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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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438 </tool> |