Mercurial > repos > rnateam > locarna_pairwise
annotate locarna_pairwise.xml @ 1:b06dc2bb3716 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
author | rnateam |
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date | Fri, 13 Jan 2017 16:49:33 -0500 |
parents | 6a79a086fa50 |
children | 433601e9f132 |
rev | line source |
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1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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1 <tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1"> |
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6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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2 <description> |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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parents:
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3 Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse) |
0
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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4 </description> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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5 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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6 <macros> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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7 <import>macros.xml</import> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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8 </macros> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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9 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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10 <expand macro="requirements" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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11 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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12 <expand macro="stdio" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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13 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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14 <expand macro="version" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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15 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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16 <command><![CDATA[ |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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17 #if str($alignment_mode.alignment_mode_selector) == "sparse" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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18 sparse |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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19 #else |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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20 locarna |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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21 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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22 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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23 '$inputA' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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24 '$inputB' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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25 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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26 --width 60 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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27 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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28 ## -------------------- alignment mode and specific options |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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29 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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30 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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31 #if str($alignment_mode.free_endgaps) != "----" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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32 --free-endgaps $alignment_mode.free_endgaps |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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33 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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34 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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35 --sequ-local on |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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36 #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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37 --struct-local on |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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38 #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
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39 --sequ-local on |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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40 --struct-local on |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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41 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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42 |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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43 @SCORING_ARGS@ |
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6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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44 |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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45 @FOLDING_ARGS@ |
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6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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46 $Folding.alifold_consensus_dp |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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47 --consensus-structure $Folding.consensus_structure |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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48 |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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49 @HEURISTIC_ARGS@ |
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6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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50 |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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51 @CONSTRAINT_ARGS@ |
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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parents:
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52 |
0
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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53 ## -------------------- output |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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54 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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55 #if 'stockholm' in str($outputs).split(",") |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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56 --stockholm '$stockholm' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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57 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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58 #if 'clustal' in str($outputs).split(",") |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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59 --clustal '$clustal' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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60 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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61 #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(",")) |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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62 --clustal '$clustal_strict' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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63 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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64 #if 'pp' in str($outputs).split(",") |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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65 --pp '$pp' |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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66 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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67 |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
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68 @STDOUT_ARGS@ |
0
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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69 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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70 #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",") |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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71 && cp $clustal $clustal_strict |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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72 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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73 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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74 #if 'clustal_strict' in str($outputs).split(",") |
1
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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75 && cp '$clustal_strict' '$clustal_strict~' |
b06dc2bb3716
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
rnateam
parents:
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76 && sed '/^#/d' '$clustal_strict~' >'$clustal_strict' |
0
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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77 #end if |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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78 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
79 ]]></command> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
80 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
81 <inputs> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
82 <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
83 help="First sequence in fasta, clustal, dp_ps, or PP2.0 format" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
84 /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
85 <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
86 help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
87 /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
88 <conditional name="alignment_mode"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
89 <param name="alignment_mode_selector" type="select" label="Alignment mode" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
90 help="Note that local alignment mode usually requires to turn off |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
91 the 'max-diff' heuristic (maximal difference for alignment traces)." |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
92 > |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
93 <option value="global_locarna">Global alignment |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
94 (LocARNA)</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
95 <option value="local_locarna">Local alignment (LocARNA)</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
96 <option value="sparse">Global alignment (SPARSE)</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
97 <option value="structure_sequence_local_locarna"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
98 Structure and sequence local alignment (LocARNA) |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
99 </option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
100 <option value="structure_local_locarna"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
101 Structure local, sequence global alignment (LocARNA) |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
|
102 </option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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changeset
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103 </param> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
104 <when value="global_locarna"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
105 <param name="free_endgaps" type="select" label="Free endgaps" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
106 help="Specify whether gaps at the ends (all, 5', or 3' ends) |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
107 of the sequences should be penalized or allowed for free."> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
108 <option value="----">None</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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109 <option value="++++">All</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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110 <option value="+-+-">5' ends</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
111 <option value="-+-+">3' ends</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
112 <option value="++--">first sequence</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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113 <option value="--++">second sequence</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
114 <option value="+---">sequence A, 5' end</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
115 <option value="-+--">sequence A, 3' end</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
116 <option value="--+-">sequence B, 5' end</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
117 <option value="---+">sequence B, 3' end</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
118 </param> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
119 </when> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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120 <when value="local_locarna"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
121 </when> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
122 <when value="sparse" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
123 <when value="structure_sequence_local_locarna" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
124 <when value="structure_local_locarna" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
125 </conditional> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
126 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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127 <param name="outputs" type="select" display="checkboxes" multiple="True" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
128 label="Output options"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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129 <option value="clustal_strict" selected="True">Output alignment |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
130 in ClustalW format</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
131 <option value="clustal" selected="False">Output alignment |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
132 in constraint-annotated ClustalW format</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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133 <option value="stockholm" selected="False">Output |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
134 alignment in Stockholm format</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
135 <option value="pp" selected="False">Output |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
136 alignment in LocARNA's PP 2.0 format</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
137 </param> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
138 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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139 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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140 <option value="--quiet">Don't report standard |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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141 output</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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142 <option value="">Non verbose</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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143 <option value="--verbose">Verbose</option> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
144 </param> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
145 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
146 <section name="Scoring" title="Scoring parameters"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
147 <expand macro="common_scoring_parameters" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
148 </section> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
149 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
150 <section name="Folding" title="RNA folding parameters"> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
151 <expand macro="common_folding_parameters" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
152 <expand macro="alifold_consensus_parameter" /> |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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153 <param name="consensus_structure" type="select" label="Consensus structure type" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
154 help="Type of consensus structures written to screen and stockholm output" |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
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|
155 > |
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156 <!-- <option value="mea">mea</option>--> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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157 <option value="none">none</option> |
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158 <option value="alifold">alifold</option> |
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159 </param> |
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160 </section> |
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161 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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162 <section name="Heuristics" title="Heuristic parameters"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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163 <expand macro="common_heuristic_parameters" /> |
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164 <expand macro="max_diff_parameters_aln" /> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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165 </section> |
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166 |
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167 <section name="Constraints" title="Constraint parameters"> |
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168 <expand macro="common_constraint_parameters" /> |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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169 </section> |
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170 </inputs> |
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171 |
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172 <outputs> |
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173 <expand macro="standard_outupt" /> |
0
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174 <data format="clustal" name="clustal" |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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175 label="${tool.name} alignment (annotated clustal) on ${on_string}"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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176 <filter>'clustal' in outputs</filter> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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177 </data> |
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178 <data format="clustal" name="clustal_strict" |
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179 label="${tool.name} alignment (clustal) on ${on_string}"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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180 <filter>'clustal_strict' in outputs</filter> |
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181 </data> |
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182 <data format="stockholm" name="stockholm" |
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183 label="${tool.name} alignment (stockholm) on ${on_string}"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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184 <filter>'stockholm' in outputs</filter> |
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185 </data> |
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186 <data format="txt" name="pp" |
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187 label="${tool.name} alignment (PP 2.0) on ${on_string}"> |
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188 <filter>'pp' in outputs</filter> |
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189 </data> |
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190 </outputs> |
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191 |
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192 <tests> |
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193 <test> |
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194 <param name="inputA" value="tRNA_2-1.fa" /> |
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195 <param name="inputB" value="tRNA_2-2.fa" /> |
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196 <param name="outputs" value="clustal" /> |
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197 <output name="clustal" file="tRNA_2.aln" lines_diff="2" /> |
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198 </test> |
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199 <test> |
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200 <param name="inputA" value="haca.snoRNA-1.aln" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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201 <param name="inputB" value="haca.snoRNA-2.aln" /> |
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202 <param name="outputs" value="clustal_strict,clustal" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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203 <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" /> |
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204 <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" /> |
0
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205 </test> |
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206 </tests> |
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207 |
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208 <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs** |
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209 |
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210 Pairwise RNA alignment tools of the LocARNA suite (locarna, |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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211 sparse). These tools perform variants of simultaneous RNA folding and |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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212 alignment. They can be adapted to specific needs by a broad range of |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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213 parameters: |
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214 |
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215 * *scoring* of the alignment, e.g. influencing the cost of |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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216 insertions/deletions and the weight of sequence vs. structure |
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217 similarity. |
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218 |
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219 * *RNA folding*, which control the secondary RNA structure prediciton. |
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220 |
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221 * *heuristics*, which trade alignment accuracy vs. computation |
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222 speed. The huge complexity of simultaneous alignment and folding |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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223 generally requires some heuristics for reasonable computation times. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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224 Some alignment instances and alignment modes will require relaxation |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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225 of the default heuristics; in particular, local, constrained, and free end gap |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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226 alignment, will often require turning off the "maximal difference for |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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227 alignment traces" heuristic. |
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228 |
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229 * *constraints*, which can be applied to include prior knowledge to |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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230 improve the quality of results and/or speed of computation. |
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231 |
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232 **Input.** |
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233 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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234 Input consists of two sequences or alignments, which are specified in |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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235 fasta, clustal, stockholm, or LocARNA pp format. |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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236 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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237 Optionally, one can specify structure and anchor constraints in these |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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238 input files. |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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239 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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240 **Output.** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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241 |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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242 The final pairwise alignment is reported in standard and/or variants of the |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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243 clustal and stockholm format, as well as LocARNA's own pp format. |
6a79a086fa50
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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244 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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245 For more information, see |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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246 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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247 ]]></help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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248 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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249 <expand macro="citations" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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250 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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251 </tool> |