Mercurial > repos > bgruening > glimmer_long_orfs

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:17:10 -0500
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16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 <tool id="glimmer_long_orfs" name="Glimmer long ORFs" version="@WRAPPER_VERSION@">
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2 <description>identify long, non-overlapping ORFs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8 long-orfs
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9 -n -t
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10 $cutoff
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11 '$inputfile'
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12 '$output'
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13 2>&1
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14 ]]></command>
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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15 <inputs>
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16 <param name="inputfile" type="data" format="fasta" label="Genome Sequence" help="Dataset missing? See TIP below"/>
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 <param name='cutoff' type='float' label='cutoff' value='1.5'/>
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18 </inputs>
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19 <outputs>
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20 <data format="tabular" name="output" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="inputfile" value='streptomyces_Tu6071_genomic.fasta'/>
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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25 <param name='cutoff' value='1.5'/>
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26 <output name="output" file='longORFSTestOutput.dat'/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30
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31 **What it does**
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32
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33 This program identifies long, non-overlapping open reading frames (orfs) in a DNA sequence file.
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 These orfs are very likely to contain genes, and can be used as a set of training sequences
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35 More specifically, among all orfs longer than a minimum length , those that do not overlap any others are output. The start codon used for
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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36 each orf is the first possible one. The program, by default, automatically determines the
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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37 value that maximizes the number of orfs that are output. With the -t option, the initial
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38 set of candidate orfs also can be filtered using entropy distance, which generally produces
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 a larger, more accurate training set, particularly for high-GC-content genomes.
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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40
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41
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42
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43 -----
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44
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45 **Glimmer Overview**
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46
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47 ::
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48
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49 ************** ************** ************** **************
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50 * * * * * * * *
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51 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
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52 * * * * * * * *
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53 ************** ************** ************** **************
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54
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55 -----
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56
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57 **Example**
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58
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59
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60 * input::
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61
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62 -Genome Sequence
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63
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64 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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65 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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66 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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67 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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68 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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69 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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70 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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71 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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72 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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73 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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74 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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75 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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76 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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77 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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78 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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79 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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80 .....
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81
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82 - Cutoff 1.5
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83
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84 * output::
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85
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86 Sequence file = /home/mohammed/galaxy-central/database/files/000/dataset_34.dat
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87 Excluded regions file = none
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88 Circular genome = true
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89 Initial minimum gene length = 90 bp
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90 Determine optimal min gene length to maximize number of genes
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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91 Maximum overlap bases = 30
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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92 Start codons = atg,gtg,ttg
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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93 Stop codons = taa,tag,tga
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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94 Sequence length = 40222
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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95 Final minimum gene length = 97
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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96
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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97 Putative Genes:
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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98 00001 40137 52 +2 0.892
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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99 00002 1319 1095 -3 0.654
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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100 00003 1555 1391 -2 0.793
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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101 00004 1953 2066 +3 1.078
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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102 00005 2045 2146 +2 0.919
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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103 00006 4463 4759 +2 0.985
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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104 00007 6785 6582 -3 1.033
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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105 00008 6862 7020 +1 0.915
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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106 00009 7300 7488 +1 0.900
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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107 00010 7463 7570 +2 0.912
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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108 00011 8399 8527 +2 1.044
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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109 00012 10652 10545 -3 0.895
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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110 00013 12170 12066 -3 1.108
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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111 00014 13891 13748 -2 0.998
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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112 00015 14157 14044 -1 1.026
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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113 00016 15285 15410 +3 0.928
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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114 00017 15829 15704 -2 0.949
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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115
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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116 ....
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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117 ]]></help>
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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118 <expand macro="citation" />
16c8bdf1037b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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119 </tool>