Mercurial > repos > gga > tripal_organism_sync

annotate macros.xml @ 4:55a94619ac51 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author gga
date Mon, 25 Feb 2019 06:15:48 -0500
parents d5cd04afe47b
children 9f1f23daff7b
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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="3.2">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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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@">3.2</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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26 <token name="@HELP_OVERVIEW@"><![CDATA[
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27 **Python-tripal Overview**
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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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33 <token name="@HELP@"><![CDATA[
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34 **Useful Links**
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36 `Tripal project website <http://tripal.info/>`_
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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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41 <token name="@DATA_DIR@">\$GALAXY_TRIPAL_SHARED_DIR</token>
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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="wait_for">
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54 <param name="wait_for"
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55 type="data"
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56 format="data"
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57 optional="true"
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58 label="Run this only after the following dataset is ready"
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59 help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/>
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60 </xml>
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61
0
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62 <xml name="test_result">
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63 <assert_stderr>
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64 <has_text text="MissingSchema" />
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65 </assert_stderr>
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66 </xml>
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67
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68 <xml name="analysis">
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69 <section name="analysis" title="Analysis" expanded="True">
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70 <param name="name"
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71 type="text"
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72 label="The analysis name [mandatory]">
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73 <expand macro="sanitized"/>
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74 </param>
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75
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76 <param name="program"
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77 type="text"
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78 label="Program name [mandatory]"
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79 help="Name of the program that was used to perform this analysis">
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80 <expand macro="sanitized"/>
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81 </param>
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82 <param name="program_version"
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83 type="text"
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84 label="Program version [mandatory]"
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85 help="Version of the program that was used to perform this analysis"/>
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86 <param name="source"
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87 type="text"
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88 label="Source name [mandatory]"
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89 help="Where this analysis comes from">
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90 <expand macro="sanitized"/>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
91 </param>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
92
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
93 <param name="source_version"
98e917aa6819 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 argument="--sourceversion"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
95 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
96 optional="True"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
97 label="Source version" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
98 <param name="source_uri"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
99 argument="--sourceuri"
98e917aa6819 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 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
101 optional="True"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
102 label="Source URI"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
103 help="URI where source data was retrieved" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
104 <param name="algorithm"
98e917aa6819 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 argument="--algorithm"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
106 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
107 label="Algorithm"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
108 optional="True"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
109 help="Algorithm of the program that was used to perform this analysis" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
110 <param name="description"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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111 argument="--description"
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diff changeset
112 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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113 optional="True"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
114 label="Analysis description">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
115 <expand macro="sanitized"/>
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116 </param>
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diff changeset
117 <param name="date"
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118 argument="--date_executed"
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diff changeset
119 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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120 optional="True"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
121 label="Execution date"
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122 help="Format: yyyy-mm-dd Default: Today">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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123 <validator type="regex" message="Date in YYYY-MM-DD format">^[0-9]{4}-[0-9]{2}-[0-9]{2}$</validator>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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124 </param>
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125 </section>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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126 </xml>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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127
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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128 <xml name="feature_rel">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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129 <param name="rel_subject_re"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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130 argument="--rel-subject-re"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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131 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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132 label="Regular expression to extract the unique name of the parent feature"
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diff changeset
133 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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134 <expand macro="sanitized"/>
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135 </param>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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136
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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137 <param name="rel_subject_type"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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138 argument="--rel-subject-type"
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139 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
140 label="Sequence type of the parent"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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141 help="this should be a Sequence Ontology term" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
142 </xml>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
143
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
144 <xml name="match_type">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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145 <param name="match_type"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
146 argument="--match-type"
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diff changeset
147 type="select"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
148 label="Match type for already loaded features">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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149 <option value="uniquename" selected="true">Unique name</option>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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150 <option value="name">Name</option>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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151 </param>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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152 </xml>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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153
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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154 <xml name="matching">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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155 <section name="matching" title="Feature matching" expanded="True">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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156 <param name="query_type"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
157 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
158 label="The feature type of the blast query"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
159 help="It must be a valid Sequence Ontology term. e.g. 'contig', 'gene', 'mRNA', 'polypeptide'" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
160
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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161 <param name="query_uniquename"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
162 type="boolean"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
163 checked="false"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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164 truevalue="--query_uniquename"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
165 falsevalue=""
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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166 label="Find blast query features using their Unique name"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
167 help="Feature name will be used otherwise" />
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
168
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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169 <param name="query_re"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
170 type="text"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
171 optional="true"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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172 label="Regular expression to extract the feature name from the blast query name"
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
173 help="leave empty if the first word in query name is sufficient">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
174 <expand macro="sanitized"/>
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175 </param>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
176 </section>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
177 </xml>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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178
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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179 <xml name="sanitized">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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180 <sanitizer>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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181 <valid initial="string.printable">
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
182 <remove value="&apos;"/>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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diff changeset
183 </valid>
98e917aa6819 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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184 <mapping initial="none">
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185 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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186 <add source="(" target="\("/>
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187 <add source=")" target="\)"/>
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188 </mapping>
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189 </sanitizer>
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190 </xml>
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191
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192 <token name="@MATCHING@"><![CDATA[
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193 #if str($matching.query_re):
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194 --query_re '${matching.query_re}'
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195 #end if
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196
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197 $matching.query_uniquename
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198
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199 --query_type '$matching.query_type'
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200 ]]></token>
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201
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202 <token name="@ANALYSIS@"><![CDATA[
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203 #if $analysis.algorithm:
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204 --algorithm '$analysis.algorithm'
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205 #end if
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206 #if $analysis.source_version:
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207 --sourceversion '$analysis.source_version'
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208 #end if
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209 #if $analysis.source_uri:
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210 --sourceuri '$analysis.source_uri'
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211 #end if
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212 #if $analysis.description:
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213 --description '$analysis.description'
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214 #end if
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215 #if $analysis.date:
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216 --date_executed '$analysis.date'
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217 #end if
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218
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219 '$analysis.name'
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220 '$analysis.program'
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221 '$analysis.program_version'
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222 '$analysis.source'
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223 ]]></token>
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224 </macros>