Mercurial > repos > rnateam > locarna_reliability_profile

annotate locarna_reliability_profile.xml @ 0:7dd1f41aee4d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
author rnateam
date Wed, 28 Dec 2016 18:52:45 -0500
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children 9942e1b7646c
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0
7dd1f41aee4d 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_reliability_profile" name="LocARNA reliability-profile" version="@VERSION@.0">
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2 <description>
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3 Plot reliability profile for probabilistic mlocarna
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4 </description>
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5
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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11
7dd1f41aee4d 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" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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13
7dd1f41aee4d 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
7dd1f41aee4d 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 (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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18 then tar xzf '$input_archive' ;
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19 else tar xf '$input_archive' ;
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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20 fi)
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21 &&
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22 reliability-profile.pl mlocarna_results
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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23
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24 --output-format='$output_format'
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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25
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26 #if $output_format == 'pdf'
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27 --out '$pdf_output_plot'
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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28 #else if $output_format == 'png'
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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29 --out '$png_output_plot'
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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30 #end if
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31
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32 #if str($title) != ""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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33 --title '$title'
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34 #end if
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35
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36 #if str($seqname) != ""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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37 --seqname $seqname
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38 #end if
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39
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40 --beta $beta
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41 --structure-weight $structure_weight
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42
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43 #if str($signals)!=""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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44 --signals '$signals'
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45 #end if
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46
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47 --offset $offset
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48
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49 #if $write_rscript:
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50 --write-R-script '$rscript_output'
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51 #end if
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52
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53 #if $write_subsequence
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54 --write-subseq
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55 #end if
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56
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57 $predict
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58 $fit_once_on
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59 $show_sw
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60 $rev_compl
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61
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62 > '$stdout'
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63 ]]></command>
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64
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65 <inputs>
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66 <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive"
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67 help="Archive of MLocARNA results (tar or tar.gz as generated by running
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68 mlocarna in probabilistic alignment mode)." />
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69
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70 <param name="title" type="text" label="Plot title"
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71 help="Title of the plot"
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72 />
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73
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74 <param name="seqname" type="text" label="Reference sequence"
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75 help="Project to a reference sequence. Provide one of the sequence names in the alignment input
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76 or leave blank to plot without projection."
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77 />
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78
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79 <param name="predict" type="boolean" checked="True"
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80 truevalue="" falsevalue="--dont-predict"
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81 argument="dont-predict"
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82 help="Turn on/off predicting."
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83 />
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84
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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85 <param name="fit_once_on" type="boolean" checked="False"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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86 truevalue="--fit-once-on" falsevalue=""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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diff changeset
87 argument="fit-once-on"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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88 help="Predict exactly one 'on'-region"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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89 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff changeset
90
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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91 <param name="show_sw" type="boolean" checked="True"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
parents:
diff changeset
92 truevalue="--show-sw" falsevalue=""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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diff changeset
93 argument="show-sw"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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94 help="Show the influence of structure weight."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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95 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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parents:
diff changeset
96
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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97 <param name="rev_compl" type="boolean" checked="False"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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98 truevalue="--revcompl" falsevalue=""
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
99 argument="revcompl"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
rnateam
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100 help="Plot and fit a reverse complement."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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101 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
102
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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103 <param argument="beta" help="Inverse temperature for fitting."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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104 type="float" value="12.0" min="1.0" max="25.0" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
105
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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106 <param name="structure_weight" argument="structure-weight"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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107 type="float" value="1.0" min="0.0" max="8.0"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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108 help="Weight of structure against sequence (1.0 means equal)"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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109 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
110
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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111 <param argument="offset" help="Genomic offset."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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112 type="integer" value="1" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
113
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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114 <param name="signals" type="text" label="List of signals"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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115 help="List of '{from to} orientation' signal specifications. Show signals in plot
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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116 and compared infered signal to them. Ranges 'from to' can be repeated;
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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117 the orientation must be either +1 or -1.
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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118 The specifications of the single signals are separated by ';'. Example of two signal,
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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119 where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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120 >
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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121 <sanitizer invalid_char=" ">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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122 <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
123 </sanitizer>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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124 </param>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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125
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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126 <param name="output_format" type="select"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
127 label="Output options">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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128 <option value="pdf" selected="True">Plot in pdf
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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129 format</option>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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130 <option value="png" selected="False">Plot in png format</option>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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131 </param>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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132
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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133 <param name="write_rscript" type="boolean" argument="write-R-script"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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134 label="Write R script" checked="False"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
135 help="Write R script that can produce the output plot."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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136 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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diff changeset
137
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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138 <param name="write_subsequence" type="boolean" argument="write-subseq"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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139 label="Write Subsequence" checked="False"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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140 help="Write subsequence in output."
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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141 />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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142
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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143 </inputs>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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144
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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145
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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146 <outputs>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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147 <data format="pdf" name="pdf_output_plot"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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148 label="${tool.name} reliability plot (pdf) ${on_string}">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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149 <filter>output_format == 'pdf'</filter>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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150 </data>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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151 <data format="png" name="png_output_plot"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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152 label="${tool.name} reliability plot (png) ${on_string}">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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153 <filter>output_format == 'png'</filter>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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154 </data>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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155 <data format="txt" name="rscript_output"
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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156 label="${tool.name} reliability plot (R script) ${on_string}">
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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157 <filter> write_rscript is True </filter>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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158 </data>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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159 <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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160 </outputs>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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161
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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162 <tests>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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163 <test>
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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164 <param name="input_archive" value="archaea.tar.gz" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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165 <param name="write_rscript" value="True" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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166 <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
7dd1f41aee4d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
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167 </test>
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168 </tests>
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169
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170 <help><![CDATA[**Reliability Profiles for Multiple RNA
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171 Alignment**
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172
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173 This tool draws reliability profiles for mlocarna alignments that have
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174 been computed in probabilistic alignment mode. Moreover, it predicts
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175 reliably aligned regions, which can be used to determine the
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176 boundaries of well conserved structured RNA motifs in less closely
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177 related sequence context.
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178
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179 **Input.**
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180 Results archive of an alignment by the mlocarna tool; for this
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181 purpose, mlocarna must be run in probabilistic mode in order to
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182 generate the required reliability information.
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183
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184 **Output.**
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185 Plot of the reliability profile for the input alignment. Moreover,
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186 a signal prediction is performed and predicted regions are
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187 annotated in the plot.
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188
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189
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190 For more information, see
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191 .. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
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192 ]]></help>
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193
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194 <expand macro="citations" />
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195
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196 </tool>