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annotate macros.xml @ 9:f45ad96c9e08 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
author gga
date Mon, 29 Jul 2019 10:08:57 -0400
parents 5559e41721c3
children c3b5bc8b4080
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1 <?xml version="1.0"?>
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2 <macros>
9
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3 <token name="@WRAPPER_VERSION@">4.0.0</token>
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4
0
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="2.7">python</requirement>
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8 <requirement type="package" version="1.65">biopython</requirement>
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9 <requirement type="package" version="0.6.2">bcbiogff</requirement>
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10 <requirement type="package" version="2.12.4">requests</requirement>
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11 <requirement type="package" version="1.11.0">six</requirement>
0
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12 <yield/>
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13 </requirements>
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14 </xml>
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15 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
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16 <token name="@EXT_URL@">
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17 "\$GALAXY_WEBAPOLLO_EXT_URL"
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18 </token>
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19 <token name="@URL@">
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20 "\$GALAXY_WEBAPOLLO_URL"
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21 </token>
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22 <token name="@ADMIN_AUTH@">
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23 "\$GALAXY_WEBAPOLLO_URL"
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24 "\$GALAXY_WEBAPOLLO_USER"
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25 "\$GALAXY_WEBAPOLLO_PASSWORD"
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26 </token>
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27
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28 <token name="@ORG_OR_GUESS@">
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29 <![CDATA[
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30 #if $org_source.source_select == "auto_json":
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31 --org_json "${org_source.org_file}"
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32 #elif $org_source.source_select == "select":
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33 --org_id "${org_source.org_select}"
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34 #else:
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35 --org_raw "${org_source.org_raw}"
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36 #end if
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37 ]]>
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38 </token>
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39 <token name="@ORG_CN_OR_GUESS@">
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40 <![CDATA[
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41 @ORG_OR_GUESS@
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42
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43 #if $cn_source.source_select == "auto":
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44 #if str($cn_source.cn_file) != "None":
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45 --seq_fasta $cn_source.cn_file
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46 #end if
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47 #else
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48 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
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49 --seq_raw
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50 #for $item in $cn_source.refseqs:
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51 "${item.refseq}"
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52 #end for
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53 #end if
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54 #end if
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55 ]]>
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56 </token>
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57 <xml name="org_or_guess">
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58 <conditional name="org_source">
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59 <param name="source_select" type="select" label="Organism Common Name Source">
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60 <option value="select">Select</option>
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61 <option value="direct">Direct Entry</option>
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62 <option value="auto_json">Autodetect from Apollo JSON</option>
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63 </param>
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64 <when value="select">
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65 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
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66 </when>
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67 <when value="direct">
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68 <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
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69 </when>
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70 <when value="auto_json">
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71 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
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72 </when>
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73 </conditional>
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74 </xml>
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75 <xml name="cn_or_guess">
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76 <expand macro="org_or_guess" />
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77 <conditional name="cn_source">
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78 <param name="source_select" type="select" label="Organism Sequence(s) Source">
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79 <option value="all">All Refseqs</option>
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80 <option value="direct">Direct Entry</option>
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81 <option value="auto">Autodetect from Fasta</option>
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82 </param>
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83 <when value="all">
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84 </when>
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85 <when value="auto">
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86 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
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87 </when>
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88 <when value="direct">
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89 <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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90 <param name="refseq" type="text" label="Reference sequence(s)" />
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91 </repeat>
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92 </when>
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93 </conditional>
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94 </xml>
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95
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96 <xml name="test_result">
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97 <assert_stderr>
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98 <has_text text="MissingSchema" />
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99 </assert_stderr>
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100 </xml>
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101
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102 <xml name="citations">
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103 <citations>
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104 <citation type="doi">10.1371/journal.pcbi.1006790</citation>
0
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105 </citations>
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106 </xml>
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107 <xml name="gff3_input">
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108 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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109 </xml>
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110 <token name="@GENOME_SELECTOR_PRE@">
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111 #if $reference_genome.reference_genome_source == 'history':
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112 ln -s $reference_genome.genome_fasta genomeref.fa;
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113 #end if
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114 </token>
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115 <token name="@GENOME_SELECTOR@">
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116 #if $reference_genome.reference_genome_source == 'cached':
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117 "${reference_genome.fasta_indexes.fields.path}"
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118 #elif $reference_genome.reference_genome_source == 'history':
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119 genomeref.fa
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120 #end if
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121 </token>
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122 <token name="@REFERENCES@">
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123 <![CDATA[
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124 ------
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125
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126 **Citation**
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127
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128 If you use this tool in Galaxy, please cite:
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129 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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130 ]]>
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131 </token>
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132 </macros>