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annotate locarna_multiple.xml @ 0:008f5c13670e draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author bgruening
date Wed, 28 Dec 2016 18:47:18 -0500
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008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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1 <tool id="locarna_multiple" name="LocARNA Multiple Aligner (mlocarna)" version="@VERSION@.0">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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2 <description>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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3 Multiple Alignment and Folding of RNAs
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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4 </description>
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5
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6 <macros>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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7 <import>macros.xml</import>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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8 </macros>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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9
008f5c13670e 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" />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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11
008f5c13670e 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" />
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13
008f5c13670e 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" />
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15
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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16 <command><![CDATA[
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17 mlocarna
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18
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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19 '$input_data'
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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20 #if 'stockholm' in str($outputs).split(","):
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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21 --stockholm
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22 #end if
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23
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24 --tgtdir mlocarna_results
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25 --width 60
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26
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27 ## -------------------- alignment mode and specific options
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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28
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29 #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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30 $alignment_mode.free_endgaps
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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31 #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
008f5c13670e 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
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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33 #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
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34 --probabilistic
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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35 $alignment_mode.consistency_transformation
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36
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37 #if str($alignment_mode.iterate) == "true"
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38 --iterate
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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39 --iterations $alignment_mode.iterations
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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40 #end if
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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41 #else if str($alignment_mode.alignment_mode_selector) == "sparse"
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42 --sparse
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43 #end if
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44
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45 ## -------------------- scoring parameters
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46
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47 --indel $Scoring.indel
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48 --indel-opening $Scoring.indel_opening
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49 --struct-weight $Scoring.struct_weight
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50 --tau $Scoring.tau
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51
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52 #if str($Scoring.sequence_score.sequence_score_selector) == "match"
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53 --match $Scoring.sequence_score.match
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54 --mismatch $Scoring.sequence_score.mismatch
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55 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
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56 --use-ribosum true
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57 #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
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58 --ribofit true
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59 #end if
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60
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61 ## -------------------- folding parameters
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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62
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63 #if $Folding.plfold_span>=0
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64 --plfold-span $Folding.plfold_span
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65 --plfold-winsize $Folding.plfold_winsize
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66 #end if
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67
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68 #if float($Folding.rnafold_temperature) != 37.0
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69 --rnafold-temperature $Folding.rnafold_temperature
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70 #end if
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71
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72 $Folding.alifold_consensus_dp
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73
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74 ## -------------------- heuristic parameters
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75
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76 -p $Heuristics.min_prob
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77 --max-diff-am $Heuristics.max_diff_am
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78 --max-diff $Heuristics.max_diff
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79 --max-diff-at-am $Heuristics.max_diff_at_am
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80 --max-bps-length-ratio $Heuristics.max_bps_length_ratio
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81
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82
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83 ## -------------------- other parameters
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84
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
diff changeset
85 #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
86 --anchor-constraints $Constraint.bed_anchors.bed_anchors_file
008f5c13670e 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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87 #end if
008f5c13670e 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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88
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
89 $Constraint.lonely_pairs
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
90
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
parents:
diff changeset
91 #if $Constraint.maxBPspan != -1
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
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diff changeset
92 --maxBPspan $Constraint.maxBPspan
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
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93 #end if
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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94
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
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diff changeset
95 $Constraint.ignore_constraints
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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96
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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97 $stdout_verbosity
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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99 #if str($stdout_verbosity) != "--quiet":
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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100 > '$stdout'
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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101 #end if
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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102
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
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103 #if 'clustal_strict' in str($outputs).split(",")
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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104 && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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105 #end if
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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106
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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107 ]]></command>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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108
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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109 <inputs>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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110 <conditional name="input_data_type">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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111 <param name="input_data_type_selector" type="select" label="Input type">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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112 <option value="fasta">Fasta input (strict)</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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113 <option value="text">Fasta-like input with LocARNA constraints</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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114 </param>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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115 <when value="fasta">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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116 <param name="input_data" type="data" format="fasta" label="Sequence input"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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117 help="Sequence input in pure fasta format"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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118 />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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119 </when>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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120 <when value="text">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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121 <param name="input_data" type="data" format="text" label="Sequence input"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 help="Sequence input in fasta format with locarna-specific extensions"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
bgruening
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123 />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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124 </when>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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125 </conditional>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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126 <conditional name="alignment_mode">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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127 <param name="alignment_mode_selector" type="select" label="Alignment mode"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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128 help="Note that local alignment mode usually requires to turn off
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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129 the 'max-diff' heuristic (maximal difference for alignment traces)."
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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130 >
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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131 <option value="global_locarna">Global alignment
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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132 (LocARNA)</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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133 <option value="local_locarna">Local alignment (LocARNA)</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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134 <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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135 <option value="sparse">Global alignment (SPARSE)</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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136 </param>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
137 <when value="global_locarna">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138 <param name="free_endgaps" type="select" label="Free endgaps"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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139 help="Specify whether gaps at the ends (all, 5', or 3' ends)
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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140 of the sequences should be penalized or allowed for free.">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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141 <option value="">No free endgaps</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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142 <option value="--free-endgaps">Free endgaps</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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143 <option value="--free-endgaps-5">Free endgaps, only 5'</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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144 <option value="--free-endgaps-3">Free endgaps, only 3'</option>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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145 </param>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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146 </when>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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147 <when value="local_locarna">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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148 </when>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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149 <when value="probabilistic">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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150 <param name="consistency_transformation" type="boolean"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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151 truevalue="--consistency-transformation" falsevalue=""
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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152 checked="true" label="Consistency transformation"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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153 help="--consistency-transformation" />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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154 <param name="iterate" type="boolean"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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155 truevalue="true" falsevalue="false"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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156 checked="false" label="Iterative refinement"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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157 help="--iterate" />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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158 <param name="iterations" type="integer"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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159 value="1" label="Number of refinement iterations"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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160 help="--iterations num" />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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161 </when>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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162 <when value="sparse" />
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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163 </conditional>
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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164
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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165 <param name="outputs" type="select" display="checkboxes" multiple="True"
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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166 label="Output options">
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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167 <option value="clustal_strict" selected="True">Output alignment
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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168 in ClustalW format</option>
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169 <option value="clustal" selected="False">Output alignment
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170 in constraint-annotated ClustalW format</option>
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171 <option value="stockholm" selected="False">Output
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172 alignment in Stockholm format</option>
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173 <option value="pp" selected="False">Output
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174 alignment in LocARNA's PP 2.0 format</option>
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175 <option value="mlocarna_results" selected="False">
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176 Output LocARNA results archive (tar.gz)</option>
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177 </param>
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178
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179 <param name="stdout_verbosity" type="select" label="Standard output verbosity">
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180 <option value="--quiet">Don't report standard
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181 output</option>
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182 <option value="">Non verbose</option>
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183 <option value="--verbose">Verbose</option>
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184 <option value="--moreverbose">More verbose</option>
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185 </param>
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186
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187 <section name="Scoring" title="Scoring parameters">
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188 <expand macro="common_scoring_parameters" />
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189 </section>
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190
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191 <section name="Folding" title="RNA folding parameters">
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192 <expand macro="plfolding_parameters" />
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193 <expand macro="common_folding_parameters" />
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194 <expand macro="alifold_consensus_parameter" />
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195 </section>
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196
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197 <section name="Heuristics" title="Heuristic parameters">
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198 <expand macro="common_heuristic_parameters" />
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199 </section>
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200
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201 <section name="Constraint" title="Constraint parameters">
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202 <expand macro="bed_anchors" />
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203 <expand macro="constraints" />
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204 </section>
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205 </inputs>
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206
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207 <outputs>
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208 <expand macro="common_outputs" />
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209 </outputs>
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210
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211 <tests>
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212 <test>
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213 <param name="input_data" value="archaea.fa" />
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214 <param name="stdout_verbosity" value="" />
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215 <output name="stdout" file="archaea-default.stdout" />
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216 </test>
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217 <test>
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218 <param name="input_data" value="haca.snoRNA.fa" />
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219 <param name="stdout_verbosity" value="" />
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220 <output name="stdout" file="haca.snoRNA-default.stdout" />
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221 </test>
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222 <test>
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223 <param name="input_data" value="archaea.fa" />
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224 <param name="stdout_verbosity" value="" />
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225 <param name="outputs" value="clustal" />
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226 <param name="alignment_mode_selector" value="probabilistic" />
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227 <output name="clustal" file="archaea-probabilistic.aln" />
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228 </test>
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229 </tests>
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230
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231 <help><![CDATA[ **MLocARNA -- Multiple alignment of RNAs**
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232
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233 MLocARNA is the (general, progressive) multiple RNA alignment tool of
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234 the LocARNA suite. It supports several alignment modes and can be
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235 adapted to specific needs by a broad range of parameters. Thus, there
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236 are parameters for
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237
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238 * *scoring* of the alignment, e.g. influencing the cost of
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239 insertions/deletions and the weight of sequence vs. structure
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240 similarity.
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241
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242 * *RNA folding*, which control the secondary RNA structure prediciton.
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243
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244 * *heuristics*, which trade alignment accuracy vs. computation
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245 speed. The huge complexity of simultaneous alignment and folding
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246 generally requires some heuristics for reasonable computation times.
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247 Some alignment instances and alignment modes will require relaxation
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248 of the default heuristics; in particular, local, constrained, and free end gap
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249 alignment, will often require turning off the "maximal difference for
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250 alignment traces" heuristic.
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251
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252 * *constraints*, which can be applied to include prior knowledge to
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253 improve the quality of results and/or speed of computation.
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254
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255 Technically, mlocarna constructs multiple alignments progressively
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256 based on pairwise alignments by locarna, locarna-p, or sparse, which
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257 perform variants of simultaneous RNA folding and alignment.
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258
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259 **Input.**
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260 Sequences can be given in plain fasta format like::
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261
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262 >fruA
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263 CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
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264 >fdhA
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265 CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
008f5c13670e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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266 >vhuU
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267 AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
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268
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269 Morover, mlocarna supports structure constraints for folding and anchor
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270 constraints for alignment. Both types of constraints can be specified
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271 in extension of the standard fasta format via 'constraint
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272 lines'. Fasta-ish input with constraints looks like this::
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273
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274 >A
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275 GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA
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276 ..((.(....xxxxxx...................))).xxx #S
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277 ..........000000.......................111 #1
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278 ..........123456.......................123 #2
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279 >B
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280 ACGGAGGGAAAGCAAGCCUUCUGCGACA
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281 .(((....xxxxxx.......))).xxx #S
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282 ........000000...........111 #1
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283 ........123456...........123 #2
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284
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285 The same anchor constraints (like by the lines tagged #1, #2) can
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286 alternatively be specified in bed format by the entries::
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287
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288 A 10 16 first_box
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289 B 8 14 first_box
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290 A 39 42 ACA-box
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291 B 25 28 ACA-box
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292
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293 where anchor regions (boxes) have arbitrary but matching names
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294 and contig/sequence names correspond to the sequence names
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295 of the fasta(-like) input.
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296
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297
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298 **Output.**
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299
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300 The final alignment is reported in standard and/or variants of the
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301 clustal and stockholm format. Moreover, an archive with final and
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302 intermediary results of the mlocarna run can be returned.
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303
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304
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305 For more information, see
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306 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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307 ]]></help>
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308
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309 <expand macro="citations" />
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310
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311 </tool>