Mercurial > repos > rnateam > viennarna_rnaalifold

annotate rnaalifold.xml @ 4:0def54ac03a6 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
author rnateam
date Tue, 18 Jul 2017 01:52:38 -0400
parents 40b99ecd575f
children
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0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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1 <tool id="viennarna_rnaalifold" name="@EXECUTABLE@" version="@VERSION@.1">
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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3 <macros>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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4 <token name="@EXECUTABLE@">RNAalifold</token>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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5 <import>macros.xml</import>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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6 </macros>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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9 <expand macro="version_command" />
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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10 <command>
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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11 <![CDATA[
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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12
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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13 RNAalifold < '$input' > '$tabularFile'
4
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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14
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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15 #if $input.ext == 'clustal':
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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16 -f C
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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17 #else if $input.ext == 'fasta':
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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18 -f F
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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19 #else if $input.ext == 'stockholm':
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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20 -f S
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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21 #else if $input.ext == 'maf':
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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22 -f M
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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23 #else:
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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24 -f C
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25 #end if
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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26 -T$model_options.temperature -d$model_options.dangling
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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27 $general_options.verbose
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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28 $general_options.color
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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29 $general_options.alignment
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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30 #if $general_options.layout_type ==0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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31 --layout-type=$general_options.layout_type
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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32 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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33 $general_options.noPS
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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34 #if str($IDs.id_prefix) <> "alignment"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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35 --id-prefix='$IDs.id_prefix'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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36 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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37 $IDs.continuous_ids
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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38 $IDs.auto_id
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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39 #if $IDs.id_digits <> 4
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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40 --id-digits=$IDs.id_digits
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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41 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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42 #if $IDs.id_start <> 1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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43 --id-start=$IDs.id_start
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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44 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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45 #if $constraints.maxBPspan <> -1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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46 --maxBPspan=$constraints.maxBPspan
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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47 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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48 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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49 --constraint='$constraints.constraintLocation.constraintsFile'
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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50 $constraints.constraintLocation.batch
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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51 $constraints.ss_cons
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52 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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53 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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54 #if len($constraints.shapeOption.shape_files) > 0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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55 #set $sf=list()
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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56 #for $i in $constraints.shapeOption.shape_files
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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57 $sf.append(str('$i.shape'))
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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58 #end for
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59 --shape= #echo ','.join($sf)
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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60 #if $constraints.shapeOption.m <> 1.8 or $constraints.shapeOption.b <> -0.6
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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61 #set $s="Dm"+str($constraints.shapeOption.m)+"b"+str($constraints.shapeOption.b)
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62 --shapeMethod=$s
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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63 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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64 #end if
4
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65 #end if
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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66
0
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67 #if $algorithm_options.pf <> "-1"
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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68 --partfunc=$algorithm_options.pf
4
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69 --pfScale=$algorithm_options.pfScale
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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70
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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71 #end if
4
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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72 #if $algorithm_options.measelect.mea == "yes":
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73 --MEA=$algorithm_options.measelect.meavalue
0def54ac03a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 746497a64b955f6b9afc1944d1c1d8d877e53267
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74 --pfScale=$algorithm_options.pfScale
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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75 #end if
4
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76
0
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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77 $algorithm_options.mis
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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78 #if $algorithm_options.stochBT_en <> 1
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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79 --stochBT_en=$algorithm_options.stochBT_en
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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80 #end if
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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81 $algorithm_options.circular
9e1a9e069a4c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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82 #if $algorithm_options.bppmThreshold <> 1e-6
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83 --bppmThreshold=$algorithm_options.bppmThreshold
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84 #end if
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85 $algorithm_options.gquad
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86 $algorithm_options.sci
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87 $model_options.notetra
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88 $model_options.nolp
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89 $model_options.nogu
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90 $model_options.noclosinggu
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91 #if $model_options.cfactor <> 1.0
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92 --cfactor=$model_options.cfactor
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93 #end if
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94 #if $model_options.nfactor <> 1.0
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95 --nfactor=$model_options.nfactor
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96 #end if
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97 $model_options.endgaps
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98 $model_options.ribosum
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99 #if $model_options.nsp
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100 --nsp='$model_options.nsp'
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101 #end if
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102 #if $model_options.betaScale <> 1.0
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103 --betaScale=$model_options.betaScale
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104 #end if
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105 && tar -cf '$imagesFile' *.ps
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106 ]]>
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107 </command>
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108 <inputs>
4
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109 <param format="clustal,fasta,stockholm,maf" name="input" type="data" label="Clustal/AlignmentFasta/Stockholm/MAF file"/>
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110
0
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111 <section name="algorithm_options" title="Algorithm Options">
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112 <param name="pf" type="select" label="Calculate partition function" help="Calculate the partition function and base pairing probability matrix in addition to the mfe structure. Default is calculation of mfe structure only." argument="-p">
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113 <option value="-1" selected="true">None</option>
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114 <option value="0">0: Deactivates the calculation of the pair probabilities, saving about 50% in runtime</option>
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115 <option value="1" >1: Calculate the partition function and base pairing probability matrix</option>
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116 </param>
4
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117
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118 <conditional name="measelect">
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119 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" argument="--MEA">
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120 <option value="no">No</option>
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121 <option value="yes">Yes</option>
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122 </param>
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123 <when value="yes">
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124 <param name="meavalue" type="float" value="1.0" label="Gamma Value" help="Calculate an MEA (maximum expected accuracy) structure. The parameter gamma tunes the importance of correctly predicted pairs versus unpaired bases. Thus, for small values of gamma the MEA structure will contain only pairs with very high probability. where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair."/>
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125 </when>
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126 </conditional>
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127
0
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128 <param argument="--mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="Output 'most informative sequence' instead of simple consensu"/>
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129 <param name="stochBT_en" type="integer" value="1" label="Number of random structures." help="Compute a certain number of random structures with a probability dependend on the partition function. Print out the energies and probabilities of the backtraced structures. " argument="--stochBT_en"/>
1
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130 <param name="pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences." argument="--pfScale"/>
0
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131 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
1
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132 <param name="bppmThreshold" type="float" value="1e-6" label="Threshold for base pair probabilities" help="By setting the threshold the base pair probabilities that are included in the output can be varied. By default only those exceeding 1e−5 in probability will be shown as squares in the dot plot. Changing the threshold to any other value allows for increase or decrease of data." argument="--bppmThreshold"/>
0
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133 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="Take into account G Quadruplex formation (-g)"/>
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134 <param name="sci" type="boolean" truevalue="--sci" falsevalue="" checked="false" label="Structure conservation index"
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135 help="Compute the structure conservation index (SCI) for the MFE consensus structure of the alignment" argument="--sci"/>
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136 </section>
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137 <section name="general_options" title="General Options">
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138 <param name="verbose" type="boolean" truevalue="--v" falsevalue="" checked="false" label=" Be verbose" argument="--v"/>
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139 <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image"
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140 help="Produce a colored version of the consensus strcture plot" argument="--color"/>
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141 <param name="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false"
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142 label="Colored and annotated alignment image"
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143 help="Produce a colored and structure annotated alignment"
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144 argument="--aln"/>
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145 <param name="layout_type" type="select" label="Layout algorithm" argument="--layout-type">
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146 <option value="1" selected="true">Default: Naview layout</option>
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147 <option value="0">Simple radial layout</option>
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148 </param>
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149 <param name="noPS" type="boolean" truevalue="" falsevalue="--noPS" checked="true" label="Produce postscript output" help="" argument="--noPS"/>
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150 </section>
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151 <section name="IDs" title="Naming Conventions">
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152 <param name="continuous_ids"
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153 type="boolean" truevalue="--continuous-ids" falsevalue="" checked="false"
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154 label="Continuous alignment ID numbering"
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155 help="Use continuous alignment ID numbering when no alignment ID can be retrieved from input data."
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156 argument="--continuous-ids"/>
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157 <param name="auto_id"
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158 type="boolean" truevalue="--auto-id" falsevalue="" checked="false"
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159 label="Automatically generate an ID for each alignment."
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160 help="If this flag is active, RNAalifold ignores any IDs retrieved from the input and automatically generates an ID for each alignment."
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161 argument="--auto-id"/>
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162 <param name="id_prefix"
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163 type="text" value="alignment"
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164 label="Prefix for automatically generated IDs (as used in output file names)"
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165 help="If this parameter is set, each alignment will be prefixed with the provided string. Hence, the output files will obey the following naming scheme: 'prefix_xxxx_ss.ps' (secondary structure plot), 'prefix_xxxx_dp.ps' (dot−plot), 'prefix_xxxx_aln.ps' (annotated alignment), etc. where xxxx is the alignment number beginning with the second alignment in the input. Use this setting in conjunction with the −−continuous−ids flag to assign IDs beginning with the first input alignment."
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166 argument="--id-prefix"/>
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167 <param name="id_digits"
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168 type="integer" value="4" min="1" max="18"
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169 label="The number of digits of the counter in automatically generated alignment IDs"
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170 help="When alignments IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left−padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]."
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171 argument="--id-digits"/>
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172 <param name="id_start"
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173 type="integer" value="1" min="0"
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174 label="First number in automatically generated alignment IDs"
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175 help="When alignment IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous alignment IDs, i.e. it activates the −−continuous−ids flag.."
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176 argument="--id-start"/>
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177 </section>
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178 <section name="constraints" title="Structure constraints">
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179 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
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180 <conditional name="constraintLocation">
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181 <param name="constraintSelector" type="select" label="Constraints" argument="--constraint">
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182 <!-- <option value="fromInput">The constraints are included in the input file</option> -->
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183 <option value="fromFile">The constraints are in a seperate file</option>
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184 <option value="none" selected="true">Don't use constraints</option>
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185 </param>
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186 <!-- <when value="fromInput"></when> -->
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187 <when value="none"></when>
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188 <when value="fromFile">
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189 <param name="constraintsFile" type="data" format="*" label="Constraints file"/>
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190 <param name="batch" type="boolean" checked="false" truevalue="--batch" falsevalue=""
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191 label="Use constraints for all alignment records"
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192 help="Usually, constraints provided from input file are only applied to a single sequence alignment. Therefore, RNAalifold will stop its computation and quit after the first input alignment was processed. Using this switch, RNAalifold processes all sequence alignments in the input and applies the same provided constraints to each of them."
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193 argument="--batch"/>
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194 <param name="ss_cons" type="boolean" checked="false" truevalue="--SS_cons" falsevalue=""
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195 label="Use consensus structures from Stockholm file (#=GF SS_cons) as constraint"
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196 help="Stockholm formatted alignment files have the possibility to store a secondary structure string in one of if ('#=GC') column annotation meta tags. The corresponding tag name is usually 'SS_cons', a consensus secondary structure. Activating this flag allows one to use this consensus secondary structure from the input file as structure constraint. Note: Activating this flag implies −−constraint."
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197 argument="--SS_cons"/>
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198 </when>
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199 </conditional>
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200 <conditional name="shapeOption">
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201 <param name="shapeSelector" type="select" label="Shape reactivity data">
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202 <option value="isUsed">Use shape reactivity data</option>
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203 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
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204 </param>
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205 <when value ="isUsed">
1
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206 <repeat name="shape_files" title="Shape File" default="0">
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207 <param type="data" name="shape" format="shape,*" label="Shape file" argument="--shape"/>
0
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208 </repeat>
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209 <param name="m" type="float" value="1.8" label="Slope m" />
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210 <param name="b" type="float" value="-0.6" label="Intercept b" help="Currently, the only data conversion method available is that of to Deigan et al 2009. This method is the default. The slope 'm' and the intercept 'b' can be set to a non−default value if necessary. Otherwise m=1.8 and b=−0.6 as stated in the paper mentioned before."/>
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211 </when>
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212 <when value="notUsed">
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213 </when>
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214 </conditional>
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215 </section>
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216 <section name="model_options" title="Model Options" expanded="true">
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217 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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218 <param name="dangling" type="select" label="How to treat dangling end energies" help="-d">
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219 <option value="0">0: ignore dangling ends</option>
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220 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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221 </param>
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222 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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223 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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224 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/>
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225 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/>
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226 <param name="cfactor" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
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227 <param name="nfactor" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
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228 <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
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229 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
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230 <param name="nsp" type="text" value="" label="Allow other pairs in addition to the usual AU,GC,and GU pairs." help="Its argument is a comma separated list of additionally allowed pairs. If the first character is '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy." argument="--nsp"/>
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231 <param name="betaScale" type="float" value="1.0" label="Scaling of Boltzman factors"
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232 help=" The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types."
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233 argument="--betaScale"/>
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234 </section>
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235 </inputs>
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236 <outputs>
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237 <data format="txt" name="tabularFile"/>
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238 <data format="tar" name="imagesFile"/>
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239 </outputs>
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240 <tests>
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241 <test>
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242 <param name="input" value="rnaalifold_input1.clustal"/>
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243 <output name="output" file="rnaalifold_result1.txt"/>
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244 </test>
4
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245 <test>
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246 <param name="input" value="rnaalifold_input1.fa"/>
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247 <output name="output" file="rnaalifold_resultfa.txt"/>
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248 </test>
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249 <test>
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250 <param name="input" value="rnaalifold_input1.stk"/>
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251 <output name="output" file="rnaalifold_resultstk.txt"/>
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252 </test>
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253 <test>
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254 <param name="input" value="rnaalifold_input1.clustal"/>
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255 <param name="mea" value="yes"/>
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256 <output name="output" file="rnaalifold_result_MEA.txt"/>
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257 </test>
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258
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259
0
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260 </tests>
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261 <help>
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262 <![CDATA[
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263 **RNAalifold**
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264
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265 -----
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266
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267 **Input format**
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268
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269 RNAalifold requires one input file
4
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270 - Clustal/AlignmentFasta/Stockholm/MAF file
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271
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272 ------
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273
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274 **Outputs**
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275
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276 - energy of the consensus structures in the clustal file
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277 - several possible postscript images bundled together in a tar file
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278
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279
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280 ]]>
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281 </help>
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282 <expand macro="citations" />
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283 </tool>