Mercurial > repos > gga > chado_feature_load_gff

annotate macros.xml @ 11:1282f881e3bf draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author gga
date Mon, 08 Jul 2019 05:38:50 -0400
parents 949ffe4ec0a8
children ab5ac677d9c6
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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="2.2.6">python-chado</requirement>
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6 <requirement type="package" version="1.5">jq</requirement>
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7 <requirement type="package" version="@PG_VERSION@">postgresql</requirement>
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8 <requirement type="package" version="0.1">pglite</requirement>
0
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9 <yield/>
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10 </requirements>
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11 </xml>
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12
11
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13 <token name="@PG_VERSION@">11.2</token>
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14
0
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15 <xml name="stdio">
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16 <stdio>
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17 <regex level="fatal" match="Exception:" source="stderr" />
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18 <regex level="fatal" match="error" source="stderr" />
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19 <exit_code range="1:" />
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20 </stdio>
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21 </xml>
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22
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23 <token name="@WRAPPER_VERSION@">2.2.6</token>
0
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25 <xml name="citation">
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26 <citations>
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27 </citations>
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28 </xml>
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29
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30 <token name="@HELP_OVERVIEW@"><![CDATA[
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31 **Python-chado Overview**
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32
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33 Python-cado provides several tools allowing to load data into a remote Chado database.
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34 ]]></token>
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35
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36 <token name="@HELP@"><![CDATA[
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37 ]]></token>
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38
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39 <xml name="sanitized">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="&apos;"/>
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43 </valid>
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44 <mapping initial="none">
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45 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
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46 <add source="(" target="\("/>
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47 <add source=")" target="\)"/>
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48 </mapping>
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49 </sanitizer>
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50 </xml>
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51
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52 <!-- I'm not proud of it, but it is needed for workflows -->
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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
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62 <xml name="feature_rel">
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63 <param name="rel_subject_re"
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64 argument="--rel-subject-re"
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65 type="text"
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66 label="Regular expression to extract the unique name of the parent feature"
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67 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature">
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68 <expand macro="sanitized"/>
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69 </param>
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70
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71 <param name="rel_subject_type"
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72 argument="--rel-subject-type"
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73 type="text"
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74 label="Sequence type of the parent"
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75 help="this should be a Sequence Ontology term" />
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76 </xml>
11
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77
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78 <xml name="psql_target">
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79 <conditional name="psql_target">
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80 <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables">
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81 <option value="remote">Remote database</option>
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82 <option value="pgtools">Database from history</option>
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83 </param>
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84 <when value="remote"/>
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85 <when value="pgtools">
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86 <param name="infile" type="data" format="postgresql" label="Input database" />
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87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/>
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88 </when>
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89 </conditional>
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90 </xml>
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91
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92 <token name="@AUTH@"><![CDATA[
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93 if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
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94 echo "__default: local" > '.auth.yml' &&
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95 echo "local:" >> '.auth.yml' &&
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96 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
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97 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
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98 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
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99 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
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100 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
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101 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
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102
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103 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
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104 ; fi
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105 ]]></token>
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106
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107 <token name="@START_PSQL@"><![CDATA[
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108 #if $psql_target.method == 'pgtools'
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109 tar -xjvf '$psql_target.infile' > /dev/null &&
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110 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
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111 #else
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112 @AUTH@
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113 #end if
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114 ]]></token>
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115
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116 <token name="@STOP_PSQL@"><![CDATA[
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117 #if $psql_target.method == 'pgtools'
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118 pglite stop -d ./postgresql &&
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119 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
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120 ;
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121 ## Make sure psql is stopped even if loading script failed
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122 pglite stop -d ./postgresql || true
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123 #end if
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124 ]]></token>
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125
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126 <token name="@ZIP_PSQL@"><![CDATA[
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127 #if $psql_target.method == 'pgtools'
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128 pglite stop -d ./postgresql &&
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129 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
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130 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null
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131 ;
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132 ## Make sure psql is stopped even if loading script failed
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133 pglite stop -d ./postgresql || true
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134 #end if
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135 ]]></token>
0
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136 </macros>