Mercurial > repos > gga > apollo_list_organism

annotate macros.xml @ 17:8dc690130172 draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author gga
date Wed, 11 Jan 2023 11:48:41 +0000
parents 78abc724d792
children
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1 <?xml version="1.0"?>
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2 <macros>
16
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3 <token name="@WRAPPER_VERSION@">4.2.13+galaxy0</token>
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4
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="4.2.13">apollo</requirement>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
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12 <token name="@EXT_URL@">
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13 "\$GALAXY_WEBAPOLLO_EXT_URL"
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14 </token>
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15 <token name="@URL@">
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16 "\$GALAXY_WEBAPOLLO_URL"
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17 </token>
10
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19 <token name="@AUTH@"><![CDATA[
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20 if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
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21 echo "__default: local" > '.auth.yml' &&
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22 echo "local:" >> '.auth.yml' &&
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23 echo " url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
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24 echo " username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
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25 echo " password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&
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26
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27 export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
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28 ; fi &&
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29 ]]></token>
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31 <token name="@ORG_OR_GUESS@">
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32 <![CDATA[
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33 #if $org_source.source_select == "auto_json":
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34 --org_json '${org_source.org_file}'
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35 #elif $org_source.source_select == "select":
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36 --org_id '${org_source.org_select}'
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37 #else:
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38 --org_raw '${org_source.org_raw}'
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39 #end if
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40 ]]>
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41 </token>
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42 <token name="@ORG_CN_OR_GUESS@">
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43 <![CDATA[
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44 @ORG_OR_GUESS@
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45
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46 #if $cn_source.source_select == "auto":
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47 #if str($cn_source.cn_file) != "None":
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48 --seq_fasta '$cn_source.cn_file'
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49 #end if
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50 #else
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51 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
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52 --seq_raw
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53 #for $item in $cn_source.refseqs:
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54 '${item.refseq}'
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55 #end for
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56 #end if
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57 #end if
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58 ]]>
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59 </token>
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60 <xml name="org_or_guess">
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61 <conditional name="org_source">
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62 <param name="source_select" type="select" label="Organism Common Name Source">
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63 <option value="select">Select</option>
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64 <option value="direct">Direct Entry</option>
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65 <option value="auto_json">Autodetect from Apollo JSON</option>
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66 </param>
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67 <when value="select">
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68 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
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69 </when>
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70 <when value="direct">
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71 <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
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72 </when>
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73 <when value="auto_json">
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74 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
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75 </when>
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76 </conditional>
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77 </xml>
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78 <xml name="cn_or_guess">
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79 <expand macro="org_or_guess" />
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80 <conditional name="cn_source">
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81 <param name="source_select" type="select" label="Organism Sequence(s) Source">
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82 <option value="all">All Refseqs</option>
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83 <option value="direct">Direct Entry</option>
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84 <option value="auto">Autodetect from Fasta</option>
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85 </param>
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86 <when value="all">
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87 </when>
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88 <when value="auto">
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89 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
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90 </when>
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91 <when value="direct">
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92 <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
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93 <param name="refseq" type="text" label="Reference sequence(s)" />
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94 </repeat>
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95 </when>
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96 </conditional>
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97 </xml>
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98
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99 <xml name="citations">
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100 <citations>
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101 <citation type="doi">10.1371/journal.pcbi.1006790</citation>
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102 </citations>
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103 </xml>
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104 <xml name="gff3_input">
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105 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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106 </xml>
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107 <token name="@GENOME_SELECTOR_PRE@">
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108 #if $reference_genome.reference_genome_source == 'history':
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109 ln -s '$reference_genome.genome_fasta' genomeref.fa;
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110 #end if
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111 </token>
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112 <token name="@GENOME_SELECTOR@">
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113 #if $reference_genome.reference_genome_source == 'cached':
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114 '${reference_genome.fasta_indexes.fields.path}'
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115 #elif $reference_genome.reference_genome_source == 'history':
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116 genomeref.fa
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117 #end if
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118 </token>
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119 <token name="@REFERENCES@">
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120 <![CDATA[
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121 ------
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122
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123 **Citation**
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124
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125 If you use this tool in Galaxy, please cite:
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126 Helena Rasche, Anthony Bretaudeau, and Mateo Boudet (2019), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
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127 ]]>
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128 </token>
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129 </macros>