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annotate glimmer_extract.xml @ 0:49cf6416bd2b draft

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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 10:17:37 -0500
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49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 <tool id="glimmer_extract" name="Extract sequence regions" version="@WRAPPER_VERSION@">
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2 <description>from a genome</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command><![CDATA[
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8 extract
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9 -t
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10 '$seqInput'
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11 '$cordInput' > '$output'
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12 2> /dev/null
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13 ]]></command>
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14 <inputs>
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15 <param name="seqInput" type="data" format="fasta" label="Genome Sequence"/>
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16 <param name="cordInput" type="data" format="tabular" label="Coordinates" help="See Help below"/>
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17 </inputs>
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18 <outputs>
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19 <data format="fasta" name="output" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="seqInput" value='streptomyces_Tu6071_genomic.fasta'/>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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24 <param name="cordInput" value='coordTest.txt'/>
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25 <output name="output" file='extractTestOutput.fasta' compare="sim_size" delta="20"/>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 </test>
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27 </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 reads a genome sequence and a list of coordinates for it and outputs a multi-
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 fasta file of the regions specified by the coordinates.
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35
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36 -----
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38 **Glimmer Overview**
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40 ::
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41
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42 ************** ************** ************** **************
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 * * * * * * * *
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44 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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45 * * * * * * * *
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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 **Example**
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51
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52
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53 * input ::
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54
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55 -Genome Sequence
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56
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57 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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58 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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59 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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60 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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61 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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62 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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63 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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64 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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65 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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66 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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67 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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68 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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69 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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70 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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71 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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72 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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73 ...
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74
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75 - Coorinates
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77 00001 40137 52 +2 0.892
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78 00002 1319 1095 -3 0.654
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79 00003 1555 1391 -2 0.793
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80 00004 1953 2066 +3 1.078
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81 00005 2045 2146 +2 0.919
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82 00006 4463 4759 +2 0.985
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83 00007 6785 6582 -3 1.033
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84 00008 6862 7020 +1 0.915
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85 00009 7300 7488 +1 0.900
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86 00010 7463 7570 +2 0.912
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87 00011 8399 8527 +2 1.044
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88 00012 10652 10545 -3 0.895
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89 00013 12170 12066 -3 1.108
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90 00014 13891 13748 -2 0.998
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91 00015 14157 14044 -1 1.026
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92 00016 15285 15410 +3 0.928
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93 00017 15829 15704 -2 0.949
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94 ...
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95
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96 * output::
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97
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98 >00001 40137 52 len=135
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99 ATGACACATTTGCTCGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAA
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100 ACCCTCTTTTTGACTTCTTCCTCCATGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCT
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101 CATTCCAAAACTCTG
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102
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103 >00002 1319 1095 len=222
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104 TTGGCTCGCCGTTTTGGAGTCCGTGCTGGAATGCCTGGCTTCATCTCAAATAAACTTTGT
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105 CCGAGTCTAACGATTGTTCCAGGAAATTACCCTAAATACACTAAAGTCAGTCGCCAATTT
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106 TCACAAATTTTCATGGAATACGATTCGGATGTTGGAATGATGTCATTGGATGAGGCATTT
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107 ATAGATTTGACAGACTATGTGGCAAGTAATACAGAAAAAAGT
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108
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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109 >00003 1555 1391 len=162
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110 ATGGAGAATCTTGAGATGAAACTGGAATCATCTAGAGATTTATCAAGAGACTGTGTTTGT
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111 ATAGATATGGATGCTTATTTTGCCGCAGTTGAAATGAGAGATAATCCTGCACTGAGAACA
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112 GTTCCTATGGCCGTAGGCTCATCGGCAATGCTGGTAAGCACC
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113
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114 >00004 1953 2066 len=111
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115 GTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCACAGATCTGTCTCG
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116 AGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCAGCGGTTGTTTTAT
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117 .....
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118 ]]></help>
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119 <expand macro="citation" />
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120 </tool>