annotate rnaplex.xml @ 3:04c56f5b0907 draft default tip

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author rnateam
date Fri, 13 Feb 2015 04:08:49 -0500
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1 <tool id="rnaplex" name="RNAplex" version="2.1.6.0">
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2 <description>Find targets of a query RNA</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <expand macro="stdio" />
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6 <macros>
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7 <token name="@EXECUTABLE@">RNAplex</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <command>
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11 <![CDATA[
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12 RNAplex
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13 #if str($clustalOption.clustalFlag) == "clustal"
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14 --alignment-mode
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15 -q$input1 -t$input2
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16 #else
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17 < $input
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18 #end if
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19 -T$temperature
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20 --interaction-length=$maxLength
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21 --extension-cost=$extensionCost
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22 --scale-accessibility=$scaleAccessibility
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23 $constraint
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24
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25
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26 #if $varExists('clustalOption.meltingOption.probeConc')
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27 --probe-mode
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28 --probe-concentration=$clustalOption.meltingOption.probeConc
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29 --na-concentration=$clustalOption.meltingOption.naConc
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30 --mg-concentration=$clustalOption.meltingOption.mgConc
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31 --k-concentration=$clustalOption.meltingOption.kConc
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32 --tris-concentration=$clustalOption.meltingOption.trisConc
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33 #end if
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34
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35
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36
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37 #if $varExists('$advancedOptions.duplexDistance')
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38 --fast-folding=$advancedOptions.fastFolding
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39 --duplex-distance=$advancedOptions.duplexDistance
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40 --energy-threshold=$advancedOptions.enThreshold
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41 #end if
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42 > $output
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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="clustalOption">
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48 <param name="clustalFlag" type="select" label="Input options">
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49 <option value="fasta" selected="true">Fasta input file</option>
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50 <option value="clustal">Clustalw input files</option>
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51 </param>
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52 <when value="fasta">
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53 <param format="fasta" name="input" type="data" label="Fasta file"/>
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54 <conditional name="meltingOption">
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55 <param name="meltingSelector" type="select" label="calculate melting temperature">
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56 <option value="no" selected="true">no</option>
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57 <option value="yes">yes</option>
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58 </param>
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59 <when value="yes">
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60 <param name="probeConc" type="float" value="0.1" label="Concentration of the probe" help="--probe-concentration"/>
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61 <param name="naConc" type="float" value="1.0" label="Na concentration" help="--na-concentration"/>
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62 <param name="mgConc" type="float" value="1.0" label="Mg concentration" help="--mg-concentration"/>
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63 <param name="kConc" type="float" value="1.0" label="K concentration" help="--k-concentration"/>
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64 <param name="trisConc" type="float" value="1.0" label="Tris concentration" help="--tris-concentration"/>
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65 </when>
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66 </conditional>
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67 </when>
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68 <when value="clustal">
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69 <param format="txt" name="input1" type="data" label="Clustal file / Query sequences"/>
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70 <param format="txt" name="input2" type="data" label="Clustal file / Target sequences"/>
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71 </when>
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72 </conditional>
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73 <param name="temperature" size="8" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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74 <param name="maxLength" type="integer" min="0" value="40" label="maximal interaction length" help="--interaction-length"/>
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75 <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
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76 <param name="extensionCost" type="integer" value="0" label="extension cost" help="--extension-cost"/>
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77 <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/>
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78 <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/>
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79
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80
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81 <conditional name="advancedOptions">
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82 <param name="advancedSelector" type="select" label="advanced options">
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83 <option value="basic">basic Options</option>
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84 <option value="advanced">advanced Options</option>
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85 </param>
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86 <when value="advanced">
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87 <param name="fastFolding" type="select" label="Backtracking" help="--fast-folding">
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88 <option value="0" selected="true">based on standard energy model (0) - normal</option>
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89 <option value="2">based on approximate plex model (2) - faster</option>
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90 <option value="1">no recomputation (1) - fastest</option>
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91 </param>
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92 <param name="duplexDistance" type="integer" value="0" label="Distance between target 3' ends of two consecutive duplexes" help="--duplex-distance"/>
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93 <param name="enThreshold" size="8" type="float" value="-100000" label="Minimum Energy Gain for a Duplex [kcal/mol]" help="--energy-threshold"/>
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94 </when>
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95 </conditional>
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96 </inputs>
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97 <outputs>
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98 <data format="txt" name="output"/>
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="input" value="rnaplex_input1.fa"/>
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103 <output name="out_file" file="rnaplex_result1.txt"/>
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104 </test>
0
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105 </tests>
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106 <help>
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107 <![CDATA[
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108
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109 **RNAplex**
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110
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111 Computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs.
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112
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113
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114 -----
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115
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116 **Input format**
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117
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118 RNALplex requires either one Fasta file or two Clustal files as input
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119
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120 ------
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121
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122 **Outputs**
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123
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124 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 range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol.
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125
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126
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127 ]]>
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128 </help>
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129 <expand macro="requirements" />
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130 </tool>