Mercurial > repos > bgruening > glimmer_extract

annotate glimmer_extract.xml @ 2:541a98e6a142 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:34:04 +0000
parents 49cf6416bd2b
children 9fbeb53b4d71
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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@">
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2 <description>from a genome</description>
2
541a98e6a142 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 extract
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10 -t
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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11 '$seqInput'
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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12 '$cordInput' > '$output'
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13 2> /dev/null
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14 ]]></command>
49cf6416bd2b 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="seqInput" type="data" format="fasta" label="Genome Sequence"/>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 <param name="cordInput" type="data" format="tabular" label="Coordinates" help="See Help below"/>
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18 </inputs>
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19 <outputs>
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20 <data format="fasta" 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="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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25 <param name="cordInput" value='coordTest.txt'/>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 <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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27 </test>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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28 </tests>
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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29
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30 <help><![CDATA[
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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31
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32 **What it does**
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33
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 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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35 fasta file of the regions specified by the coordinates.
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36
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37 -----
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38
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39 **Glimmer Overview**
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40
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41 ::
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42
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43 ************** ************** ************** **************
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44 * * * * * * * *
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45 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 *
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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 **Example**
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52
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53
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54 * input ::
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55
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56 -Genome Sequence
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57
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58 CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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59 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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60 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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61 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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62 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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63 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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64 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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65 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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66 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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67 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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68 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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69 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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70 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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71 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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72 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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73 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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74 ...
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75
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76 - Coorinates
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78 00001 40137 52 +2 0.892
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79 00002 1319 1095 -3 0.654
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80 00003 1555 1391 -2 0.793
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81 00004 1953 2066 +3 1.078
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82 00005 2045 2146 +2 0.919
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83 00006 4463 4759 +2 0.985
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84 00007 6785 6582 -3 1.033
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85 00008 6862 7020 +1 0.915
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86 00009 7300 7488 +1 0.900
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87 00010 7463 7570 +2 0.912
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88 00011 8399 8527 +2 1.044
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89 00012 10652 10545 -3 0.895
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90 00013 12170 12066 -3 1.108
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91 00014 13891 13748 -2 0.998
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92 00015 14157 14044 -1 1.026
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93 00016 15285 15410 +3 0.928
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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94 00017 15829 15704 -2 0.949
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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95 ...
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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96
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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97 * output::
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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98
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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99 >00001 40137 52 len=135
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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100 ATGACACATTTGCTCGTTGCTTTGACCCACTACGAGGCCAGTATCATGATTTCTAGAAAA
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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101 ACCCTCTTTTTGACTTCTTCCTCCATGATCCTTGTAGATTTTGAATTTGAAGTTTTTTCT
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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102 CATTCCAAAACTCTG
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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103
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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104 >00002 1319 1095 len=222
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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105 TTGGCTCGCCGTTTTGGAGTCCGTGCTGGAATGCCTGGCTTCATCTCAAATAAACTTTGT
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106 CCGAGTCTAACGATTGTTCCAGGAAATTACCCTAAATACACTAAAGTCAGTCGCCAATTT
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107 TCACAAATTTTCATGGAATACGATTCGGATGTTGGAATGATGTCATTGGATGAGGCATTT
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108 ATAGATTTGACAGACTATGTGGCAAGTAATACAGAAAAAAGT
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109
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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110 >00003 1555 1391 len=162
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111 ATGGAGAATCTTGAGATGAAACTGGAATCATCTAGAGATTTATCAAGAGACTGTGTTTGT
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112 ATAGATATGGATGCTTATTTTGCCGCAGTTGAAATGAGAGATAATCCTGCACTGAGAACA
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113 GTTCCTATGGCCGTAGGCTCATCGGCAATGCTGGTAAGCACC
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114
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115 >00004 1953 2066 len=111
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116 GTGCGCGAGAAAAAACTACGCGTTAACCGCCAATTTTCACTTCCCCACAGATCTGTCTCG
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117 AGATTCTCGAGTCATTTTTCAAGTTTATTTGTTTGTCAGCGGTTGTTTTAT
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118 .....
49cf6416bd2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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119 ]]></help>
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120 <expand macro="citation" />
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121 </tool>