Mercurial > repos > gga > tripal_analysis_add_analysis

annotate macros.xml @ 0:f8dab3351d1b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:49:35 -0400
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f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.0.4">python-tripal</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9
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10 <xml name="stdio">
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11 <stdio>
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12 <regex level="fatal" match="Exception:" source="stderr" />
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13 <regex level="fatal" match="error" source="stderr" />
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14 <exit_code range="1:" />
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15 </stdio>
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16 </xml>
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17
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18 <token name="@WRAPPER_VERSION@">2.0.4</token>
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20 <xml name="citation">
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21 <citations>
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22 <citation type="doi">10.1093/database/bat075</citation>
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23 </citations>
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24 </xml>
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25
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26 <token name="@HELP_OVERVIEW@"><![CDATA[
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27 **Python-tripal Overview**
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28
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29 Python-tripal provides several tools allowing to load data into a remote Chado-based Tripal database.
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30 The tripal_rest_api Tripal module must be installed on the remote server to use these tools.
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31 ]]></token>
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32
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33 <token name="@HELP@"><![CDATA[
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34 **Useful Links**
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35
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36 `Tripal project website <http://tripal.info/>`_
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37
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38 `Tripal REST API module <http://github.com/abretaud/tripal_rest_api>`_: a Tripal module required to use these galaxy tools
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39 ]]></token>
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40
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41 <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
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42
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43 <token name="@AUTH@"><![CDATA[
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44 echo "__default: local" > '.auth.yml' &&
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45 echo "local:" >> '.auth.yml' &&
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46 echo " tripal_url: \"\$GALAXY_TRIPAL_URL\"" >> '.auth.yml' &&
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47 echo " username: \"\$GALAXY_TRIPAL_USER\"" >> '.auth.yml' &&
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48 echo " password: \"\$GALAXY_TRIPAL_PASSWORD\"" >> '.auth.yml' &&
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49
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50 TRIPAILLE_GLOBAL_CONFIG_PATH='.auth.yml'
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51 ]]></token>
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52
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53 <xml name="test_result">
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54 <assert_stderr>
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55 <has_text text="MissingSchema" />
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56 </assert_stderr>
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57 </xml>
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58
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59 <xml name="analysis">
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60 <section name="analysis" title="Analysis" expanded="True">
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61 <param name="name"
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62 type="text"
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63 label="The analysis name [mandatory]">
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64 <expand macro="sanitized"/>
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65 </param>
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66
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67 <param name="program"
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68 type="text"
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69 label="Program name [mandatory]"
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70 help="Name of the program that was used to perform this analysis">
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71 <expand macro="sanitized"/>
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72 </param>
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73 <param name="program_version"
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74 type="text"
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75 label="Program version [mandatory]"
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76 help="Version of the program that was used to perform this analysis"/>
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77 <param name="source"
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78 type="text"
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79 label="Source name [mandatory]"
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80 help="Where this analysis comes from">
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81 <expand macro="sanitized"/>
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82 </param>
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83
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84 <param name="source_version"
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85 argument="--sourceversion"
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86 type="text"
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87 optional="True"
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88 label="Source version" />
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89 <param name="source_uri"
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90 argument="--sourceuri"
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diff changeset
91 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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92 optional="True"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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93 label="Source URI"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
94 help="URI where source data was retrieved" />
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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95 <param name="algorithm"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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96 argument="--algorithm"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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97 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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98 label="Algorithm"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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99 optional="True"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
100 help="Algorithm of the program that was used to perform this analysis" />
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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101 <param name="description"
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102 argument="--description"
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103 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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104 optional="True"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
105 label="Analysis description">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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106 <expand macro="sanitized"/>
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107 </param>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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108 <param name="date"
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109 argument="--date_executed"
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110 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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111 optional="True"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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112 label="Execution date"
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113 help="Format: yyyy-mm-dd Default: Today">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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114 <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
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115 </param>
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116 </section>
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117 </xml>
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118
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119 <xml name="feature_rel">
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120 <param name="rel_subject_re"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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121 argument="--rel-subject-re"
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122 type="text"
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123 label="Regular expression to extract the unique name of the parent feature"
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124 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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125 <expand macro="sanitized"/>
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126 </param>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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127
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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128 <param name="rel_subject_type"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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129 argument="--rel-subject-type"
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130 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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131 label="Sequence type of the parent"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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132 help="this should be a Sequence Ontology term" />
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
133 </xml>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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134
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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135 <xml name="match_type">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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136 <param name="match_type"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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137 argument="--match-type"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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138 type="select"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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139 label="Match type for already loaded features">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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140 <option value="uniquename" selected="true">Unique name</option>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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141 <option value="name">Name</option>
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142 </param>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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143 </xml>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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144
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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145 <xml name="matching">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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146 <section name="matching" title="Feature matching" expanded="True">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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147 <param name="query_type"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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148 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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149 label="The feature type of the blast query"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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150 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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151
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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152 <param name="query_uniquename"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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153 type="boolean"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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154 checked="false"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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155 truevalue="--query_uniquename"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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156 falsevalue=""
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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157 label="Find blast query features using their Unique name"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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158 help="Feature name will be used otherwise" />
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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159
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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160 <param name="query_re"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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161 type="text"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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162 optional="true"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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163 label="Regular expression to extract the feature name from the blast query name"
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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164 help="leave empty if the first word in query name is sufficient">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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165 <expand macro="sanitized"/>
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166 </param>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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167 </section>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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168 </xml>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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169
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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170 <xml name="sanitized">
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171 <sanitizer>
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172 <valid initial="string.printable">
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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173 <remove value="&apos;"/>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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174 </valid>
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175 <mapping initial="none">
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176 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
f8dab3351d1b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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177 <add source="(" target="\("/>
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178 <add source=")" target="\)"/>
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179 </mapping>
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180 </sanitizer>
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181 </xml>
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182
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183 <token name="@MATCHING@"><![CDATA[
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184 #if str($matching.query_re):
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185 --query_re '${matching.query_re}'
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186 #end if
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187
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188 $matching.query_uniquename
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189
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190 --query_type '$matching.query_type'
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191 ]]></token>
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192
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193 <token name="@ANALYSIS@"><![CDATA[
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194 #if $analysis.algorithm:
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195 --algorithm '$analysis.algorithm'
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196 #end if
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197 #if $analysis.source_version:
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198 --sourceversion '$analysis.source_version'
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199 #end if
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200 #if $analysis.source_uri:
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201 --sourceuri '$analysis.source_uri'
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202 #end if
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203 #if $analysis.description:
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204 --description '$analysis.description'
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205 #end if
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206 #if $analysis.date:
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207 --date_executed '$analysis.date'
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208 #end if
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209
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210 '$analysis.name'
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211 '$analysis.program'
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212 '$analysis.program_version'
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213 '$analysis.source'
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214 ]]></token>
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215 </macros>