Mercurial > repos > rnateam > locarna_multiple
annotate locarna_multiple.xml @ 2:94b0468f0db8 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author | rnateam |
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date | Sat, 21 Jan 2017 17:38:28 -0500 |
parents | a5a2d3cefce1 |
children | 7554c0df9139 |
rev | line source |
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1
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner" version="@VERSION@.1"> |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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2 <description> |
1
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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3 Multiple Alignment and Folding of RNAs (mlocarna) |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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4 </description> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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5 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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6 <macros> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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7 <import>macros.xml</import> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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8 </macros> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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9 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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10 <expand macro="requirements" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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11 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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12 <expand macro="stdio" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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13 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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14 <expand macro="version" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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15 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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16 <command><![CDATA[ |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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17 mlocarna |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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18 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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19 '$input_data' |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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20 #if 'stockholm' in str($outputs).split(","): |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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21 --stockholm |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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22 #end if |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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23 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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24 --tgtdir mlocarna_results |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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25 --width 60 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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26 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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27 ## -------------------- alignment mode and specific options |
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a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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28 # |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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30 $alignment_mode.free_endgaps |
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a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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31 #elif str($alignment_mode.alignment_mode_selector) == "local_locarna" |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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32 --sequ-local on |
1
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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33 #elif str($alignment_mode.alignment_mode_selector) == "probabilistic" |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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34 --probabilistic |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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35 $alignment_mode.consistency_transformation |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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36 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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37 #if str($alignment_mode.iterate) == "true" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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38 --iterate |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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39 --iterations $alignment_mode.iterations |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 #end if |
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a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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41 #elif str($alignment_mode.alignment_mode_selector) == "sparse" |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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42 --sparse |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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43 #end if |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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44 |
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a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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45 @SCORING_ARGS@ |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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46 |
1
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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47 @FOLDING_ARGS@ |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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48 #if $Folding.plfold_span>=0 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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49 --plfold-span $Folding.plfold_span |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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50 --plfold-winsize $Folding.plfold_winsize |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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51 #end if |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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52 $Folding.alifold_consensus_dp |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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53 |
1
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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54 @HEURISTIC_ARGS@ |
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94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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55 |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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56 #if str($alignment_mode.alignment_mode_selector) == "sparse" |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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57 --pw-aligner-options " @HEURISTIC_SPARSE_ARGS@ " |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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58 #end if |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
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59 |
0
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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60 |
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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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61 @CONSTRAINT_ARGS@ |
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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62 #if str($Constraints.bed_anchors.bed_anchors_selector) == "yes" |
a5a2d3cefce1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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63 --anchor-constraints $Constraints.bed_anchors.bed_anchors_file |
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8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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64 #end if |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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65 |
1
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
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66 @STDOUT_ARGS@ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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67 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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68 #if 'clustal_strict' in str($outputs).split(",") |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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69 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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70 #end if |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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71 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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72 ]]></command> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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73 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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74 <inputs> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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75 <conditional name="input_data_type"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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76 <param name="input_data_type_selector" type="select" label="Input type"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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77 <option value="fasta">Fasta input (strict)</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
78 <option value="text">Fasta-like input with LocARNA constraints</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
79 </param> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
80 <when value="fasta"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
81 <param name="input_data" type="data" format="fasta" label="Sequence input" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
82 help="Sequence input in pure fasta format" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
83 /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
84 </when> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
85 <when value="text"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
86 <param name="input_data" type="data" format="text" label="Sequence input" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
87 help="Sequence input in fasta format with locarna-specific extensions" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
88 /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
89 </when> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
90 </conditional> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
91 <conditional name="alignment_mode"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
92 <param name="alignment_mode_selector" type="select" label="Alignment mode" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
93 help="Note that local alignment mode usually requires to turn off |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
94 the 'max-diff' heuristic (maximal difference for alignment traces)." |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
95 > |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
96 <option value="global_locarna">Global alignment |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
97 (LocARNA)</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
98 <option value="local_locarna">Local alignment (LocARNA)</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
99 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option> |
2
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
changeset
|
100 <option value="sparse">Global fast alignment (SPARSE)</option> |
0
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
101 </param> |
8414fea2a6fd
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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102 <when value="global_locarna"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
103 <param name="free_endgaps" type="select" label="Free endgaps" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
104 help="Specify whether gaps at the ends (all, 5', or 3' ends) |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
105 of the sequences should be penalized or allowed for free."> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
106 <option value="">No free endgaps</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
107 <option value="--free-endgaps">Free endgaps</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
108 <option value="--free-endgaps-5">Free endgaps, only 5'</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
109 <option value="--free-endgaps-3">Free endgaps, only 3'</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
110 </param> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
111 </when> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
112 <when value="local_locarna"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
113 </when> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
114 <when value="probabilistic"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
115 <param name="consistency_transformation" type="boolean" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
116 truevalue="--consistency-transformation" falsevalue="" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
117 checked="true" label="Consistency transformation" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
118 help="--consistency-transformation" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
119 <param name="iterate" type="boolean" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
120 truevalue="true" falsevalue="false" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
121 checked="false" label="Iterative refinement" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
122 help="--iterate" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
123 <param name="iterations" type="integer" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
124 value="1" label="Number of refinement iterations" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
125 help="--iterations num" /> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
126 </when> |
2
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
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|
127 <when value="sparse"> |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
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|
128 <section name="HeuristicsSparse" title="Heuristic parameters for SPARSE"> |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
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|
129 <expand macro="common_heuristic_parameters_sparse" /> |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
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|
130 </section> |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
diff
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|
131 </when> |
94b0468f0db8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
rnateam
parents:
1
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|
132 |
0
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
133 </conditional> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
134 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
135 <param name="outputs" type="select" display="checkboxes" multiple="True" |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
136 label="Output options"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
137 <option value="clustal_strict" selected="True">Output alignment |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
138 in ClustalW format</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
139 <option value="clustal" selected="False">Output alignment |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
140 in constraint-annotated ClustalW format</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
141 <option value="stockholm" selected="False">Output |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
142 alignment in Stockholm format</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
143 <option value="pp" selected="False">Output |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
changeset
|
144 alignment in LocARNA's PP 2.0 format</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
145 <option value="mlocarna_results" selected="False"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
146 Output LocARNA results archive (tar.gz)</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
147 </param> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
148 |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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|
149 <param name="stdout_verbosity" type="select" label="Standard output verbosity"> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
150 <option value="--quiet">Don't report standard |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
151 output</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff
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|
152 <option value="">Non verbose</option> |
8414fea2a6fd
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
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153 <option value="--verbose">Verbose</option> |
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154 <option value="--moreverbose">More verbose</option> |
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155 </param> |
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156 |
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157 <section name="Scoring" title="Scoring parameters"> |
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158 <expand macro="common_scoring_parameters" /> |
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159 </section> |
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160 |
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161 <section name="Folding" title="RNA folding parameters"> |
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162 <expand macro="plfolding_parameters" /> |
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163 <expand macro="common_folding_parameters" /> |
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164 <expand macro="alifold_consensus_parameter" /> |
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165 </section> |
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166 |
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167 <section name="Heuristics" title="Heuristic parameters"> |
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168 <expand macro="common_heuristic_parameters" /> |
1
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169 <expand macro="max_diff_parameters_aln" /> |
0
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170 </section> |
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171 |
1
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172 <section name="Constraints" title="Constraint parameters"> |
0
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173 <expand macro="bed_anchors" /> |
1
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174 <expand macro="common_constraint_parameters" /> |
0
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175 </section> |
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176 </inputs> |
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177 |
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178 <outputs> |
1
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179 <expand macro="mlocarna_outputs" /> |
0
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180 </outputs> |
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181 |
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182 <tests> |
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183 <test> |
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184 <param name="input_data" value="archaea.fa" /> |
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185 <param name="stdout_verbosity" value="" /> |
1
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186 <param name="max_diff_mode_selector" value="max-diff" /> |
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187 <param name="max_diff" value="20" /> |
0
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188 <output name="stdout" file="archaea-default.stdout" /> |
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189 </test> |
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190 <test> |
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191 <param name="input_data" value="haca.snoRNA.fa" /> |
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192 <param name="stdout_verbosity" value="" /> |
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193 <output name="stdout" file="haca.snoRNA-default.stdout" /> |
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194 </test> |
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195 <test> |
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196 <param name="input_data" value="archaea.fa" /> |
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197 <param name="stdout_verbosity" value="" /> |
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198 <param name="outputs" value="clustal" /> |
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199 <param name="alignment_mode_selector" value="probabilistic" /> |
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200 <output name="clustal" file="archaea-probabilistic.aln" /> |
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201 </test> |
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202 <test> |
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203 <param name="input_data" value="archaea.fa" /> |
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204 <param name="stdout_verbosity" value="" /> |
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205 <param name="outputs" value="clustal" /> |
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206 <param name="max_diff_mode_selector" value="max-diff-aln" /> |
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207 <param name="max_diff_aln" value="archaea-ref.aln" /> |
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208 <param name="max_diff" value="2" /> |
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209 <output name="clustal" file="archaea-ref_result.aln" /> |
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210 </test> |
0
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211 </tests> |
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212 |
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213 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs** |
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214 |
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215 MLocARNA is the (general, progressive) multiple RNA alignment tool of |
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216 the LocARNA suite. It supports several alignment modes and can be |
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217 adapted to specific needs by a broad range of parameters. Thus, there |
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218 are parameters for |
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219 |
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220 * *scoring* of the alignment, e.g. influencing the cost of |
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221 insertions/deletions and the weight of sequence vs. structure |
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222 similarity. |
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223 |
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224 * *RNA folding*, which control the secondary RNA structure prediciton. |
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225 |
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226 * *heuristics*, which trade alignment accuracy vs. computation |
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227 speed. The huge complexity of simultaneous alignment and folding |
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228 generally requires some heuristics for reasonable computation times. |
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229 Some alignment instances and alignment modes will require relaxation |
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230 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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231 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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232 alignment traces" heuristic. |
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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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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 * *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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235 improve the quality of results and/or speed of computation. |
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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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236 |
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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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237 Technically, mlocarna constructs multiple alignments progressively |
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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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238 based on pairwise alignments by locarna, locarna-p, or sparse, which |
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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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239 perform variants of simultaneous RNA folding and alignment. |
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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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240 |
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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 **Input.** |
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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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242 Sequences can be given in plain fasta format like:: |
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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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243 |
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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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244 >fruA |
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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 CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG |
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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 >fdhA |
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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 CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG |
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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 >vhuU |
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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 AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU |
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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 Morover, mlocarna supports structure constraints for folding and anchor |
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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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252 constraints for alignment. Both types of constraints can be specified |
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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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253 in extension of the standard fasta format via 'constraint |
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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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254 lines'. Fasta-ish input with constraints looks like this:: |
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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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255 |
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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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256 >A |
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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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257 GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA |
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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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258 ..((.(....xxxxxx...................))).xxx #S |
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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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259 ..........000000.......................111 #1 |
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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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260 ..........123456.......................123 #2 |
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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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261 >B |
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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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262 ACGGAGGGAAAGCAAGCCUUCUGCGACA |
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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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263 .(((....xxxxxx.......))).xxx #S |
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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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264 ........000000...........111 #1 |
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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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265 ........123456...........123 #2 |
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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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266 |
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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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267 The same anchor constraints (like by the lines tagged #1, #2) can |
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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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268 alternatively be specified in bed format by the entries:: |
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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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269 |
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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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270 A 10 16 first_box |
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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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271 B 8 14 first_box |
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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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272 A 39 42 ACA-box |
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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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273 B 25 28 ACA-box |
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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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274 |
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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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275 where anchor regions (boxes) have arbitrary but matching names |
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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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276 and contig/sequence names correspond to the sequence names |
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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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277 of the fasta(-like) input. |
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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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278 |
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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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279 |
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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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280 **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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281 |
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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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282 The final alignment is reported in standard and/or variants of the |
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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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283 clustal and stockholm format. Moreover, an archive with final 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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284 intermediary results of the mlocarna run can be returned. |
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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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285 |
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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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286 |
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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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287 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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288 .. __: 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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289 ]]></help> |
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290 |
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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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291 <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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292 |
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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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293 </tool> |