Mercurial > repos > rnateam > viennarna_rnasnoop

annotate rnasnoop.xml @ 0:113b9e77bd35 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
author rnateam
date Wed, 05 Oct 2016 16:41:57 -0400
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113b9e77bd35 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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1 <tool id="viennarna_rnasnoop" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description> Find targets of a query H/ACA snoRNA</description>
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3
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4 <macros>
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5 <token name="@EXECUTABLE@">RNAsnoop</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 RNAsnoop --query='$input1' --target='$input2' > '$output'
113b9e77bd35 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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14 --alignmentLength=$length
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15 $constraint
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16 --energy-threshold=$energyThreshold
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17 #if $varExists('$advancedOptions.extensioncost')
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18 $advancedOptions.fast
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19 --extension-cost=$advancedOptions.extensioncost
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20 --minimal-right-duplex=$advancedOptions.minrightduplex
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21 --minimal-loop-energy=$advancedOptions.minloop
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22 --minimal-left-duplex=$advancedOptions.minleftduplex
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23 --minimal-duplex=$advancedOptions.minduplex
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24 --duplex-distance=$advancedOptions.duplexdist
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25 --minimal-stem-length=$advancedOptions.minstemlength
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26 --maximal-stem-length=$advancedOptions.maxstemlength
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27 --minimal-duplex-box-length=$advancedOptions.minbox
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28 --maximal-duplex-box-length=$advancedOptions.maxbox
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29 --minimal-snoRNA-stem-loop-length=$advancedOptions.minsnornastem
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30 --maximal-snoRNA-stem-loop-length=$advancedOptions.maxsnornastem
113b9e77bd35 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 78112b796295701aabd1ee2268983222f0d27374
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31 --minimal-snoRNA-duplex-length=$advancedOptions.minsnornaduplex
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32 --maximal-snoRNA-duplex-length=$advancedOptions.maxsnornaduplex
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33 --minimal-duplex-stem-energy=$advancedOptions.minduplexstem
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34 --minimal-total-energy=$advancedOptions.mintotal
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35 --maximal-stem-asymmetry=$advancedOptions.maxstemasymmetry
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36 --minimal-lower-stem-energy=$advancedOptions.minstemenergy
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37 #end if
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38 #if $filetypeOptions.filetypeSelector == "fasta"
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39 && tar -cf '$imagesFile' *.ps
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40 #else
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41 --alignment-mode
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42 #end if
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43 ]]>
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44 </command>
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45
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46 <inputs>
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47 <conditional name="filetypeOptions">
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48 <param name="filetypeSelector" type="select" label="Select Filetype">
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49 <option value="fasta" selected="true">Fasta</option>
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50 <option value="clustal">Clustal</option>
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51 </param>
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52 <when value="fasta">
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53 <param format="fasta" name="input1" type="data" label="Query sequences"/>
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54 <param format="fasta" name="input2" type="data" label="Target sequences"/>
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55 </when>
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56 <when value="clustal">
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57 <param format="txt" name="input1" type="data" label="Query sequences"/>
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58 <param format="txt" name="input2" type="data" label="Target sequences"/>
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59 </when>
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60 </conditional>
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61
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62 <param name="length" type="integer" min="0" value="25" label="Maximal alignment length" help="--alignmentLength"/>
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63 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate the stem structure subject to constraints" help="--constraint"/>
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64 <param name="energyThreshold" type="float" value="-1.0" label="Maximal energy difference between the mfe and the desired suboptimal structure" help="--energy-threshold"/>
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65
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66 <conditional name="advancedOptions">
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67 <param name="advancedSelector" type="select" label="advanced options">
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68 <option value="basic">basic Options</option>
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69 <option value="advanced">advanced Options</option>
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70 </param>
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71 <when value="advanced">
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72 <param name="fast" type="boolean" truevalue="--fast-folding=1" falsevalue="--fast-folding=0" checked="true" label="Backtracking based on the standard energy model" help="--fast-folding"/>
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73 <param name="extensioncost" type="integer" value="0" label="Cost to add each nucleotide in a duplex" help="--extension-cost"/>
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74 <param name="minrightduplex" type="integer" value="-270" label="Minimal right duplex energy" help="--minimal-right-duplex"/>
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75 <param name="minloop" type="integer" value="-280" label="Minimal Loop energy" help="--minimal-loop-energy"/>
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76 <param name="minleftduplex" type="integer" value="-170" label="Minimal left duplex energy" help="--minimal-left-duplex"/>
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77 <param name="minduplex" type="integer" value="-1090" label="Minimal duplex energy" help="--minimal-duplex"/>
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78 <param name="duplexdist" type="integer" value="2" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
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79 <param name="minstemlength" type="integer" value="5" label="Minimal snoRNA stem length" help="--minimal-stem-length"/>
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80 <param name="maxstemlength" type="integer" value="120" label="Maximal snoRNA stem length" help="--maximal-stem-length"/>
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81 <param name="minbox" type="integer" value="11" label="Minimal distance between the duplex end and the H/ACA box" help="--minimal-duplex-box-length"/>
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82 <param name="maxbox" type="integer" value="16" label="Maximal distance between the duplex end and the H/ACA box" help="--maximal-duplex-box-length"/>
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83 <param name="minsnornastem" type="integer" value="1" label="Minimal distance between the stem loop and the snoRNA sequence" help="--minimal-snoRNA-stem-loop-length"/>
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84 <param name="maxsnornastem" type="integer" value="100000" label="Maximal distance between the stem loop and the snoRNA sequence" help="--maximal-snoRNA-stem-loop-length"/>
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85 <param name="minsnornaduplex" type="integer" value="0" label="Minimal distance between the duplex and the snoRNA sequence" help="--minimal-snoRNA-duplex-length"/>
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86 <param name="maxsnornaduplex" type="integer" value="0" label="Maximal distance between the duplex and the snoRNA sequence" help="--maximal-snoRNA-duplex-length"/>
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87 <param name="minduplexstem" type="integer" value="-1370" label="Minimal duplex stem energy" help="--minimal-duplex-stem-energy"/>
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88 <param name="mintotal" type="integer" value="100000" label="Minimal total energy" help="--minimal-total-energy"/>
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89 <param name="maxstemasymmetry" type="integer" value="30" label="Maximal snoRNA stem asymmetry" help="--maximal-stem-asymmetry"/>
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90 <param name="minstemenergy" type="integer" value="100000" label="Minimal lower stem energy" help="--minimal-lower-stem-energy"/>
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91 </when>
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92 <when value="basic">
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93 </when>
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94 </conditional>
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95 </inputs>
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96 <outputs>
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97 <data format="txt" name="output"/>
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98 <data format="tar" name="imagesFile">
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99 <filter>filetypeOptions['filetypeSelector'] == "fasta"</filter>
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100 </data>
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101
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102 </outputs>
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103 <tests>
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104 <test>
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105 <param name="input1" value="rnasnoop_input1b.fa"/>
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106 <param name="input2" value="rnasnoop_input1a.fa"/>
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107 <output name="output" file="rnasnoop_result1.txt"/>
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108 </test>
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109 </tests>
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110 <help>
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111 <![CDATA[
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112
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113 **RNAsnoop**
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114
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115 reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively and computes optimal and suboptimal secondary structures for their hybridization. The calculation can be done roughly done in O(nm), where is n the length of the target sequence and m is the length of the snoRNA stem, as it is specially tailored to the special case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex.
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116
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117
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118 -----
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119
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120 **Input format**
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121
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122 RNAsnoop requires two input files
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123
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124 - either two Fasta files
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125 - or two Clustal alignment files
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126
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127 ------
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128
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129 **Outputs**
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130
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131 The computed optimal and suboptimal structure are given, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent intermolecular interactions between the snoRNA and its target.
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132 The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. If available the opening energy are also returned.
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133
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134
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135 ]]>
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136 </help>
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137 <expand macro="citations" />
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138 </tool>