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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
author iuc
date Mon, 16 Dec 2024 14:41:26 +0000
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d6e786f3b225 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit a80e3e4aa3a40970af507bf9119cf7f1c2ffb336
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1 <tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@" profile="@PROFILE_VERSION@">
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2 <description>from a GenBank file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
4
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9 python '$__tool_directory__/glimmer_gbk_to_orf.py'
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10 -g '$infile'
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11 -a '$aa_output'
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12 -n '$nc_output'
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13 ##TODO translation table, can be extracted from genbank file directly
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14 ]]></command>
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15 <inputs>
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16 <param name="infile" type='data' format="genbank" label="gene bank file"/>
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17 </inputs>
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18 <outputs>
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19 <data name="aa_output" format="fasta" label="${tool.name} on ${on_string}: Amino acids"/>
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20 <data name="nc_output" format="fasta" label="{tool.name} on ${on_string}: Nucleotides"/>
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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="infile" value="test.gbk" />
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25 <output name="aa_output" file="orf_aa.fa" />
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26 <output name="nc_output" file="orf_nc.fa" />
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31 Read a GenBank file and export fasta formatted amino acid and CDS files.
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32
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33 -----
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34
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35 **Example**
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36 * input::
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37
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38 Genebankfile
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39
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40 LOCUS BA000030 9025608 bp DNA linear BCT 21-DEC-2007
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41 DEFINITION Streptomyces avermitilis MA-4680 DNA, complete genome.
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42 ACCESSION BA000030 AP005021-AP005050
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43 VERSION BA000030.3 GI:148878541
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44 DBLINK Project: 189
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45 KEYWORDS .
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46 SOURCE Streptomyces avermitilis MA-4680
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47 ORGANISM Streptomyces avermitilis MA-4680
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48 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
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49 Streptomycineae; Streptomycetaceae; Streptomyces.
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50 REFERENCE 1
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51 AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
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52 Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
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53 Kikuchi,H., Shiba,T., Sakaki,Y. and Hattori,M.
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54 TITLE Genome sequence of an industrial microorganism Streptomyces
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55 avermitilis: deducing the ability of producing secondary
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56 metabolites
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57 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 98 (21), 12215-12220 (2001)
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58 PUBMED 11572948
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59 REFERENCE 2
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60 AUTHORS Ikeda,H., Ishikawa,J., Hanamoto,A., Shinose,M., Kikuchi,H.,
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61 Shiba,T., Sakaki,Y., Hattori,M. and Omura,S.
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62 TITLE Complete genome sequence and comparative analysis of the industrial
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63 microorganism Streptomyces avermitilis
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64 JOURNAL Nat. Biotechnol. 21 (5), 526-531 (2003)
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65 PUBMED 12692562
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66 REFERENCE 3 (bases 1 to 9025608)
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67 AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
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68 Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
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69 Kushida,N., Shiba,T., Sakaki,Y. and Hattori,M.
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70 TITLE Direct Submission
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71 JOURNAL Submitted (29-MAR-2002) Contact:S Omura Kitasato University,
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72 Kitasato Institute for Life Sciences; 1-15-1 Kitasato, Sagamihara,
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73 Kanagawa 228-8555, Japan URL
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74 :http://avermitilis.ls.kitasato-u.ac.jp/
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75 COMMENT On Jun 15, 2007 this sequence version replaced gi:57546753.
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76 This work was done in collaboration with Haruo Ikeda(*1), Jun
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77 Ishikawa(*2), Akiharu Hanamoto(*3), Chigusa Takahashi(*3), Mayumi
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78 Shinose(*3), Hiroshi Horikawa(*4), Hidekazu Nakazawa(*4), Tomomi
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79 Osonoe(*4), Norihiro Kushida(*4), Hisashi Kikuchi(*4), Tadayoshi
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80 Shiba(*5), Yoshiyuki Sakaki(*6,*7), Masahira Hattori(*1,*7)
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81 and Satoshi Omura(*1,*3).
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82 Final finishing process and all annotation were done by H. Ikeda
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83 and J. Ishikawa.
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84 *1 Kitasato Institute for Life Sciences, Kitasato University *2
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85 National Institute of Infectious Diseases
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86 *3 The Kitasato Institute
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87 *4 National Institute of Technology and Evaluation *5 School of
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88 Science, Kitasato University
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89 *6 Institute of Medical Science, University of Tokyo *7 RIKEN,
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90 Genomic Sciences Center
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91 All the annotated genes identified are available from following
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92 urls.
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93 http://avermitilis.ls.kitasato-u.ac.jp.
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94 FEATURES Location/Qualifiers
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95 source 1..9025608
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96 /organism="Streptomyces avermitilis MA-4680"
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97 /mol_type="genomic DNA"
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98 /strain="MA-4680"
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99 /db_xref="taxon:227882"
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100 /note="This strain is also named as strain: ATCC 31267,
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101 NCIMB 12804 or NRRL 8165."
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102 gene complement(1380..1811)
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103 /locus_tag="SAV_1"
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104 CDS complement(1380..1811)
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105 /locus_tag="SAV_1"
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106 /codon_start=1
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107 /transl_table=11
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108 /product="hypothetical protein"
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109 /protein_id="BAC67710.1"
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110 /db_xref="GI:29603637"
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111 /translation="MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQA
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112 AAAAEDAALNYMPGVLARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARL
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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113 MHTQEEKEAPPKSFKEKLRSALDGPQPPEPAGRPWKPGSET"
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114
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115
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116 * output::
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117
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118 - aminoAcidOutput
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119 >SAV_1
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120 MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQAAAAAEDAALNYMPGVL
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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121 ARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARLMHTQEEKEAPPKSFKEKL
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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122 RSALDGPQPPEPAGRPWKPGSET
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123 >SAV_2
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124 VPPQGARGTIVSATGSGKTSMAAASTLNCFPEGRILVTVPTLDLLAQTAQAWRAVGHHSP
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125 MIAVCSLENDPVLNERT
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126 >SAV_3
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127 MDWNFPDDDIFFCGGCGDDDTPDPRVPRQDKALCVRCDRVERQVRRYRITVPRRNAIMRF
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128 QRDVCALCQEGPPTDHCPDAVSFWHIDHDHRCCPPGGSCGRCVRGLLCLPCNATRLPAYE
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129 RLPNVLRDSPRFNTYLNSPPARHPEARPTARDHAGPRDASSYLIDAFFTAADHPEGNALS
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130 S
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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131 >SAV_4
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132 VALTPGGTRVTQWQDRQAIGDMHERRVAAALRARGWTVQPCGQGTYPPAVREALRRTRSA
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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133 LRHFPDLIAARGADLITIDAKDRMPSTDTDRYAVSADTVTAGLFFTAAHAPTPLYYVFGD
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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134 LKVLTPAEVVHYTAHALRHRSGAFHLVRTEQAHCFDDVFGSAGAAAAA
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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135 >SAV_5
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136 MMLLMAAYVDPRFRPTLWPGTPVPTPELMPLRGARADGEWIVWTPQVRSRSHTVPVPEDF
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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137 YLREFMEVDPEDLDAVAALMGAYGHLGGSINTGSWDVDVYERLKELTEREHPRAPFALHG
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138 ELATLFMREAQAAITTWLALRREGGLDALIEPEVSEEELAQWQASNADLEEAWPRDLDHL
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139 RELSLEIRISNLVSELNAALKPFSIGIGGLGDRYPTILAVAFLQLYNHLAEDATIRECAN
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140 ETCRRHFVRQRGRAAYGQNRTSGIKYCTRECARAQAQREHRRRRKQQTTTLQQPPAPGPQ
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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141 SHDTSEPTAEGR
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142 >SAV_6
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143 MISLREHQVEANARIRAWAGFPTRSPVPAQGLRGTVVSATGSGKTITAAWAARECFRGGR
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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144 ILVMVPTLDLLVQTAQAWRRVGHNGPMVAACSLEKDEVLEQLGVRTTTNPIQLALWAGHG
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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145 PVVVFATYASLVDREDPEDVTGRAKVRGPLEAALAGGQRLYGQTMDGFDLAVVDEAHSTT
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146 GDLGRPWAAIHDNSRIPADFRLYLTATPRILASPRPQKGADGRELEIATMASDPDGPYGE
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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147 WLFELGLSEAVERGILAGFEIDVLEIRDPSPALGESEEAQRGRRLALLQTALLEHAAARN
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148 LRTVMTFHQRVEEAAAFAQTMPQTAARLYEAEVSAEALVDAGALPESSIGAEFYELEAGR
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149 HVPPDRVWAAWLCGDHLVAERREVLRQFADGLDAGNKRVHRAFLASVRVLGEGVDIVGER
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150 GVEAICFADTRGSQVEIVQNIGRALRPNPDGTNKTARIIVPVFLQPGENPTDMVASASFA
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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151 PLVTVLQGLRSHSERLVEQLASRALTSGQRHVHVKRDEDGRIIGTTTEGEGGQHESEGAV
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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152 ESALLHFSTPRDATTIAAFLRTRVYRPESLVWLEGYQALLRWRKKNHITGLYAVPYDTET
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153 EAGVTKAFPLGRWVHQQRRTYRAGELDPHRTTLLDEAGMVWEPGDEAWENKLAALRSFHR
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154 AHGHLAPRRDAVWGDADSELVPVGEHMANLRRKDGLGKNPQRAATRATQLAAIDPDWNCP
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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155 WPLDWQRHYRVLADLATDEPHSRLPDIQPGVQFEGDDLGKWLQRQRRSWAELSEEQQQRL
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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156 TALGVTPAEPPTPTPSAKGGGKAAAFQRGLAALAQWIQREGAHKVVPRGHVEAVVIDGQE
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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157 HQHKLGVWISNTKTRRDKLTHDQRTALAALGVEWA
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158 ....
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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159
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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160 - orfs
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161
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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162 >SAV_1
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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163 ATGACCGCCGAGTGGTACGTCCTCGTCGAAGAGGACACACGAGAGACCAAGCGCGCCGAC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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164 GGCGTTGAACTCAGATTGCACCGCTGGAAACTGGCGGCCACTCAGCACATCGCAGGAGAT
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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165 CAGGAACAGGCCGCCGCCGCGGCCGAGGATGCGGCCCTGAACTACATGCCGGGAGTGCTC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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166 GCTCGGCATGCCCGACCGGGAGACGAACCGGCCCGGCATGCTTTCCTCACCCAGGACGGG
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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167 GCCTGGCTGGTGCTCCTCAGGCAGCGGCACCGCGAGTGTCACATACGGGTGACCACTGCC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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168 CGGCTCATGCATACACAGGAAGAGAAGGAGGCCCCGCCGAAAAGCTTCAAGGAGAAACTC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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169 CGCAGCGCCCTGGATGGTCCTCAGCCGCCCGAACCGGCTGGTAGGCCATGGAAGCCGGGC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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170 AGCGAAACCTGA
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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171 >SAV_2
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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172 GTGCCCCCTCAGGGAGCCCGTGGCACGATCGTGTCAGCTACCGGGTCCGGCAAAACGAGC
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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173 ATGGCCGCCGCGAGCACGCTGAACTGCTTCCCCGAAGGCCGGATCCTCGTGACCGTGCCG
9ef16934fa8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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174 ACCCTGGACCTGCTCGCACAGACCGCCCAGGCGTGGCGGGCAGTCGGCCACCACTCCCCC
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175 ATGATCGCGGTGTGCTCGCTGGAGAACGACCCAGTGCTGAACGAGCGGACCTGA
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176 >SAV_3
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177 ATGGACTGGAACTTCCCCGACGACGACATCTTCTTCTGCGGCGGGTGCGGCGACGACGAC
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178 ACCCCCGACCCGCGGGTCCCGCGTCAGGACAAGGCCCTGTGCGTCCGCTGCGACAGAGTC
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179 GAACGGCAGGTCCGCCGATACCGGATCACCGTGCCGCGGAGGAACGCGATCATGCGCTTC
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180 CAGCGCGACGTCTGCGCCCTGTGCCAGGAAGGCCCGCCGACCGACCACTGCCCCGATGCC
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181 GTCAGCTTCTGGCACATCGACCACGACCACCGCTGCTGCCCTCCCGGCGGCTCATGCGGG
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182 CGGTGCGTCCGCGGCCTCCTGTGCCTGCCCTGCAACGCCACCCGCCTGCCCGCCTACGAA
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183 CGCCTCCCCAACGTCCTCCGCGACAGCCCTCGCTTCAACACCTACCTCAACAGCCCACCC
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184 GCCCGGCACCCCGAAGCCCGCCCCACCGCCAGGGACCATGCAGGCCCCCGCGACGCATCC
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185 AGCTACCTCATCGACGCCTTTTTCACCGCCGCGGACCATCCCGAGGGGAACGCCCTCAGC
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186 TCCTGA
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187 >SAV_4
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188 GTGGCACTTACCCCAGGGGGAACCCGAGTGACGCAGTGGCAGGACCGCCAGGCGATAGGC
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189 GACATGCACGAACGTCGGGTGGCGGCCGCGCTGCGCGCCCGCGGCTGGACCGTCCAGCCC
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190 TGCGGACAGGGCACCTACCCGCCCGCCGTACGGGAAGCCCTGCGCCGGACCCGCTCCGCC
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191 CTGCGGCACTTCCCCGACCTCATCGCCGCCCGCGGCGCCGACCTGATCACCATCGACGCC
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192 AAGGACCGCATGCCCAGCACCGACACCGACCGCTACGCCGTCAGCGCCGACACCGTGACC
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193 GCCGGCCTCTTTTTCACCGCGGCCCACGCTCCGACTCCGCTGTACTACGTCTTCGGCGAC
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194 CTGAAGGTCCTCACGCCGGCGGAGGTGGTCCACTACACCGCTCACGCCTTGCGCCACCGC
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195 AGCGGTGCCTTCCACCTCGTACGCACGGAGCAAGCACACTGCTTCGACGACGTCTTCGGA
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196 TCGGCTGGCGCAGCAGCTGCGGCATGA
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197 >SAV_5
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198 ATGATGCTCCTCATGGCGGCATACGTTGACCCACGCTTTCGTCCTACGCTATGGCCTGGA
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199 ACGCCCGTGCCGACACCGGAGTTGATGCCTCTTCGCGGAGCGCGGGCCGACGGTGAATGG
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200 ATCGTCTGGACCCCGCAGGTCCGCTCCCGCTCGCACACGGTCCCCGTGCCGGAGGACTTC
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201 TACCTGCGCGAGTTCATGGAGGTCGACCCTGAGGACCTCGACGCCGTGGCCGCCCTGATG
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202 GGCGCCTACGGACACCTCGGCGGGAGCATCAACACCGGAAGCTGGGACGTCGACGTCTAC
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203 GAGCGCCTCAAGGAGCTCACGGAGCGCGAACACCCCCGCGCGCCGTTCGCCCTGCACGGC
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204 GAACTGGCCACGCTGTTCATGAGGGAGGCGCAGGCGGCCATCACCACCTGGCTGGCCCTG
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205 CGCCGCGAGGGCGGGCTCGACGCGCTCATCGAGCCCGAGGTGTCCGAGGAAGAACTGGCG
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206 CAGTGGCAAGCGAGCAACGCTGATCTTGAGGAAGCGTGGCCGCGGGACCTGGACCACCTG
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207 CGCGAACTCTCCCTGGAGATCAGGATCAGCAACCTCGTGAGCGAACTGAACGCCGCGCTG
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208 AAGCCGTTCAGCATCGGCATCGGCGGCCTGGGCGACCGCTACCCCACCATCCTCGCTGTG
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209 GCGTTCCTCCAGCTCTACAACCACCTCGCCGAGGACGCCACGATCCGCGAGTGCGCGAAC
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210 GAGACCTGCCGCCGCCACTTCGTACGCCAGCGCGGCCGCGCCGCATACGGGCAGAACCGC
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211 ACCAGCGGCATCAAGTACTGCACCCGCGAATGCGCCCGCGCCCAGGCCCAGCGCGAACAC
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212 CGCCGGCGCCGCAAACAGCAGACCACGACCCTCCAGCAGCCGCCGGCGCCTGGTCCTCAG
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213 TCTCACGACACCTCAGAGCCGACTGCCGAAGGGCGCTGA
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214 .......
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215
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216 ]]></help>
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217 <expand macro="citation" />
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218 </tool>