Mercurial > repos > rnateam > rnalien

annotate rnalien.xml @ 3:9e173f038156 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien commit eb542d372ee6b1bc6653424fa44fa25cb40c99df-dirty
author rnateam
date Sun, 12 Mar 2017 11:23:48 -0400
parents f8aa5646a7c6
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1 <tool id="RNAlien" name="RNAlien" version="1.3.6">
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2 <description>
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3 Unsupervised covariance model construction from a single input sequence
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.3.6">rnalien</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive"><![CDATA[
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9 RNAlien
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10 -i '$input_sequence'
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11 #if $t
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12 -t $t
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13 #end if
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14 -o `pwd`
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15 -d outdir
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16 -c "\${GALAXY_SLOTS:-4}"
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17 -z $z
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18 -e $e
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19 -b $blast_database
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20 -x=False
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21 $s
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22 $f
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23 $a
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24 > 'warnings'
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="input_sequence" type="data" format="fasta" label="Input sequence"/>
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29 <param argument="-t" type="integer" value=""
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30 label="NCBI taxonomy id of input organism" optional="true"/>
0
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31 <param argument="-z" type="float" value="1.0" min="0.1"
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32 label="Only candidate sequences with a nSCI higher than this value are accepted." help=""/>
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33 <param argument="-e" type="float" value="0.001" min="0.000000000001"
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34 label="Evalue cutoff for cmsearch filtering" help=""/>
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35 <param name="blast_database" type="select" label="Specify name of blast database to use."
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36 help="Blast databases, e.g. nt, refseq_genomic,..">
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37 <option value="nt">nt</option>
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38 <option value="refseq_genomic">refseq_genomic</option>
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39 <option value="refseq_rna">refseq_rna</option>
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40 <option value="refseq_representative_genomes">refseq_representative_genomes</option>
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41 </param>
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42 <param argument="-a" truevalue="-a" falsevalue="" checked="True" type="boolean"
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43 label="Filter blast hits by coverage of at least 80%." help=""/>
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44 <param argument="-s" truevalue="-s" falsevalue="" checked="False" type="boolean"
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45 label="Only the best blast hit per taxonomic entry is considered." help=""/>
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46 <param argument="-f" truevalue="-f" falsevalue="" checked="True" type="boolean"
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47 label="Toggles blast softmasking, meaning exclusion of low complexity (repetative) regions in lookup table." help=""/>
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48 </inputs>
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49 <outputs>
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50 <data format="txt" name="log" from_work_dir="./outdir/Log" label="RNAlien construction summary"/>
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51 <data format="cm" name="cm" from_work_dir="./outdir/result.cm" label="RNAlien result covariance model"/>
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52 <data format="stockholm" name="stockholm" from_work_dir="./outdir/result.stockholm" label="RNAlien result stockholm alignment"/>
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53 <data format="clustal" name="clustal" from_work_dir="./outdir/result.clustal" label="RNAlien result clustal alignment"/>
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54 <data format="fasta" name="sequences" from_work_dir="./outdir/result.fa" label="RNAlien result sequences"/>
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55 <data format="txt" name="warnings" from_work_dir="warnings" label="Warnings from tool dependencies"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="input_sequence" value="tcvh4.fa"/>
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60 <param name="taxonomy_id" value="10239"/>
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61 <output name="warnings" file="warnings"/>
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62 </test>
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63 </tests>
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64 <help>
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65
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66 <![CDATA[
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67
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68 **What it does**
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69
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70 RNAlien is a tool for automatic construction of RNAfamily models from a single sequence.
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71
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72 **Input**
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73
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74 Example:
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75
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76 >AJ243001.2
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77
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78 ATACTTACCTGGCACAGGGGATACCACGATCACCAAGGTGGTTCCCCCAAGACGAGGCTC
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79
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80 ACCATTGCACTCCGGTGGCGCTGACCCTTGCAATGACCCCAAATGTGGGTTACTCGGGTG
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81
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82 TGTAATTTCTGTTAGCTGGGGACTGCGTTCGCGCTTTCCCCTT
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83
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84 **Options**
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85 -i Path to input fasta file
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86 -o Path to output directory
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87 -t NCBI taxonomy ID number of input RNA organism
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88 -z Only candidate sequences with a nSCI higher than this value are accepted. 1.0
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89 -e Evalue cutoff for cmsearch filtering. 0.001
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90 -b Specify name of blast database to use. nt
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91 -a Filter blast hits by coverage of at least 80%. True
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92 -s Only the best blast hit per taxonomic entry is considered. False
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93 -f Toggles blast softmasking, meaning exclusion of low complexity (repetative) regions in lookup table. True
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94 -r Restrict search space to taxonomic kingdom (bacteria,archea,eukaryia).
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95
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96 **Output**
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97
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98 RNAlien collects potential family members in multiple iterations.
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99
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100 The output of RNAlien consists of a stockholm alignment, a covariance
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101
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102 model and a Log file.
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103
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104 For further questions please refer to the RNAlien Help page.
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105
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106 .. _Userguide: http://nibiru.tbi.univie.ac.at/rnalien/help _.
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107
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108 ]]>
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109
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110 </help>
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111 <citations>
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112 <citation type="doi">10.1093/nar/gkw558</citation>
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113 </citations>
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114 </tool>