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annotate macros.xml @ 8:df7a90763b3c draft default tip

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 37aa8fa02c144220da9a3899644025b8c19697c9
author eric-rasche
date Tue, 27 Jun 2017 04:13:27 -0400
parents f9a6e151b3b4
children
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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1 <?xml version="1.0"?>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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2 <macros>
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3 <xml name="requirements">
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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4 <requirements>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package" version="1.65">biopython</requirement>
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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7 <requirement type="package" version="0.6.2">bcbiogff</requirement>
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eric-rasche
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8 <requirement type="package" version="2.12.4">requests</requirement>
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df7a90763b3c planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 37aa8fa02c144220da9a3899644025b8c19697c9
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9 <requirement type="package" version="0.16.0">future</requirement>
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10 <yield/>
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11 </requirements>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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12 </xml>
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13 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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14 <token name="@EXT_URL@">
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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15 \$GALAXY_WEBAPOLLO_EXT_URL
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16 </token>
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17 <token name="@URL@">
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c8e16c8eff98 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 6944305517dcccad3e6b37f8aba0b43ccb004540
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18 \$GALAXY_WEBAPOLLO_URL
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19 </token>
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20 <token name="@ADMIN_AUTH@">
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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21 \$GALAXY_WEBAPOLLO_URL
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22 \$GALAXY_WEBAPOLLO_USER
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23 \$GALAXY_WEBAPOLLO_PASSWORD
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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24 </token>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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25
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26 <token name="@ORG_OR_GUESS@">
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27 <![CDATA[
3
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28 #if $org_source.source_select == "auto_json":
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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29 --org_json "${org_source.org_file}"
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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30 #elif $org_source.source_select == "select":
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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31 --org_id "${org_source.org_select}"
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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32 #else:
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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33 --org_raw "${org_source.org_raw}"
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34 #end if
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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35 ]]>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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36 </token>
3
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37 <token name="@ORG_CN_OR_GUESS@">
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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38 <![CDATA[
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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39 @ORG_OR_GUESS@
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40
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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41 #if $cn_source.source_select == "auto":
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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42 #if str($cn_source.cn_file) != "None":
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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43 --seq_fasta $cn_source.cn_file
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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44 #end if
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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45 #else
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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46 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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47 --seq_raw
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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48 #for $item in $cn_source.refseqs:
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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49 "${item.refseq}"
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50 #end for
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51 #end if
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52 #end if
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53 ]]>
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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54 </token>
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parents: 2
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55 <xml name="org_or_guess">
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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56 <conditional name="org_source">
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57 <param name="source_select" type="select" label="Organism Common Name Source">
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58 <option value="select">Select</option>
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59 <option value="direct">Direct Entry</option>
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60 <option value="auto_json">Autodetect from Apollo JSON</option>
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61 </param>
3
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62 <when value="select">
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63 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
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64 </when>
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65 <when value="direct">
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66 <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
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67 </when>
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68 <when value="auto_json">
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69 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
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70 </when>
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71 </conditional>
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72 </xml>
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73 <xml name="cn_or_guess">
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74 <expand macro="org_or_guess" />
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75 <conditional name="cn_source">
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76 <param name="source_select" type="select" label="Organism Sequence(s) Source">
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77 <option value="all">All Refseqs</option>
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78 <option value="direct">Direct Entry</option>
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79 <option value="auto">Autodetect from Fasta</option>
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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80 </param>
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81 <when value="all">
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82 </when>
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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parents: 2
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83 <when value="auto">
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84 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
0
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85 </when>
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86 <when value="direct">
3
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87 <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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88 <param name="refseq" type="text" label="Reference sequence(s)" />
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89 </repeat>
0
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90 </when>
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91 </conditional>
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92 </xml>
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93
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94 <xml name="citations">
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95 <citations>
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96 </citations>
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97 </xml>
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98 <xml name="gff3_input">
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99 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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100 </xml>
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101 <token name="@GENOME_SELECTOR_PRE@">
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102 #if $reference_genome.reference_genome_source == 'history':
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103 ln -s $reference_genome.genome_fasta genomeref.fa;
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104 #end if
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105 </token>
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106 <token name="@GENOME_SELECTOR@">
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107 #if $reference_genome.reference_genome_source == 'cached':
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108 "${reference_genome.fasta_indexes.fields.path}"
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109 #elif $reference_genome.reference_genome_source == 'history':
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110 genomeref.fa
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111 #end if
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112 </token>
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113 <token name="@REFERENCES@">
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114 <![CDATA[
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115 ------
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116
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117 **Citation**
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118
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119 If you use this tool in Galaxy, please cite:
7
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120 Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
0
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121 ]]>
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122 </token>
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123 </macros>