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annotate rnaz.xml @ 1:e23c455f8335 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e02ab52f82468dc7751e6564bdf6e959bbba3a65
author bgruening
date Wed, 01 Mar 2017 17:15:13 -0500
parents 8abf4c0a4af0
children 580ee1e91801
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1 <tool id="rnaz" name="RNAz" version="2.1.0">
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2 <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.1">rnaz</requirement>
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6 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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10 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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11 </stdio>
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13 <version_command>RNAz --version</version_command>
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14 <command>
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15 <![CDATA[
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16 RNAz '$input'
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17 --$forward_or_reverse
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18 $dinucleotide
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19 $mononucleotide
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20 $locarnate
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21 $noshuffle
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22 #if $cutoff != -1.0:
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23 --cutoff=$cutoff
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24 #end if
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25 > temp.txt &&
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26 grep -v -E "^ |^#|^$" temp.txt > '$outfile' &&
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27 grep -E "^ |^#|^$" temp.txt
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param format="txt" name="input" type="data" label="Input Alignment File" />
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32 <param name="forward_or_reverse" type="select" label="Scored strand">
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33 <option value="forward">Score forward strand (-f)</option>
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34 <option value="reverse">Score reverse strand (-r)</option>
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35 <option value="both-strands">Score both strands (-b)</option>
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36 </param>
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37 <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/>
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38 <param argument="--dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" />
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39 <param argument="--mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores" />
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40 <param argument="--locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" />
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41 <param argument="--no-shuffle" name="noshuffle" type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling" />
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42 </inputs>
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43 <outputs>
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44 <data name="outfile" format="fasta" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input" value="rnaz_input_trna.aln"/>
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49 <output name="outfile" file="rnaz_result_trna.fasta"/>
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50 </test>
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51 <test>
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52 <param name="input" value="rnaz_test_input2.aln"/>
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53 <output name="outfile" file="rnaz_result2.fasta"/>
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58
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59 **What it does**
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60
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61 RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs.
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62
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63 **Input**
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64
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65 Input is a multiple sequence alignment file. Currently the the following alignment formats can be read: CLUSTALW, FASTA, PHYLIP,NEXUS, MAF, and XMFA. Alignments can be generated by any sequence based alignment program. Sequence alignment tools can be found in Galaxy too (e.g. ClustalW).
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66
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67 Example:
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68
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69 CLUSTAL 2.1 multiple sequence alignment
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70
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71
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72 sacCer1 GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
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74 sacKlu GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGCTAGGGGTTCGAGC
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75
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76 sacBay GCCTTGTTGGCGCAATCGGTAGCGCGTATGACTCTTAATCATAAGGTTAGGGGTTCGAGC
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78 sacCas GCTTCAGTAGCTCAGTCGGAAGAGCGTCAGTCTCATAATCTGAAGGTCGAGAGTTCGAAC
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80 \** * * \** \** \**\** \** \**\** * *\** \**\**\* *\**\* * \**\**\** *
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82
1
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83 **Output**
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84
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85 In Galaxy RNAz gives you 2 output files: a summary file and a result file. For the example input they look like this:
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86
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87 Summary:
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88
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89 Sequences: 4
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90 Columns: 60
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91 Reading direction: forward
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92 Mean pairwise identity: 82.50
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93 Shannon entropy: 0.28395
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94 G+C content: 0.51667
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95 Mean single sequence MFE: -16.67
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96 Consensus MFE: -15.59
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97 Energy contribution: -15.53
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98 Covariance contribution: -0.06
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99 Combinations/Pair: 1.26
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100 Mean z-score: -0.66
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101 Structure conservation index: 0.93
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102 Background model: mononucleotide
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103 Decision model: sequence based alignment quality
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104 SVM decision value: -0.64
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105 SVM RNA-class probability: 0.238023
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106 Prediction: OTHER
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107
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108
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109 Result file:
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110
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111 >sacCer1
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112
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113 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
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114
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115 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
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116
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117 >sacKlu
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118
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119 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGCUAGGGGUUCGAGC
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120
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121 ..((((...((((........))))....((((((((..(....)..)))))))))))). ( -16.00, z-score = -0.11, R)
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122
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123 >sacBay
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124
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125 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
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126
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127 ..((((...((((........))))....(((((((((((....))))))))))))))). ( -19.00, z-score = -1.44, R)
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128
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129 >sacCas
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130
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131 GCUUCAGUAGCUCAGUCGGAAGAGCGUCAGUCUCAUAAUCUGAAGGUCGAGAGUUCGAAC
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132
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133 .((((((..((((........))))..............)))))).(((......))).. ( -12.69, z-score = 0.35, R)
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134
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135 >consensus
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136
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137 GCCUUGUUGGCGCAAUCGGUAGCGCGUAUGACUCUUAAUCAUAAGGUUAGGGGUUCGAGC
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138
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139 ..((((...((((........))))....(((((((((((....))))))))))))))). (-15.59 = -15.53 + -0.06)
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140
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141
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142
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143
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144
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145
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146 ]]>
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147
0
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148 </help>
1
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149
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150 <citations>
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151 <citation type="doi">10.1142/9789814295291_0009</citation>
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152 </citations>
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153
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154 </tool>