Mercurial > repos > gga > tripal_organism_add_organism

annotate organism_add_organism.xml @ 3:92407294b12e draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1
author gga
date Mon, 06 Aug 2018 04:44:48 -0400
parents 56390a41953e
children 2d707e97598b
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56390a41953e 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 <tool id="organism_add_organism" profile="16.04" name="Create an organism" version="@WRAPPER_VERSION@.0">
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3 <description>in Tripal</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.5">jq</requirement>
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9 </expand>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12
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13 @AUTH@
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56390a41953e planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 tripaille organism add_organism
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16
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17 #if str($description):
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18 --comment '$description'
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19 #end if
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21 #if $infra.use_infra:
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22 --infraspecific_rank '$infra.rank'
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23 --infraspecific_name '$infra.name'
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24 #end if
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25
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26 '$genus'
3
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27 '$species'
0
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28 '$common'
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29 '$abbr'
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30
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31 | jq -S . > $results
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32 ]]></command>
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33 <inputs>
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34 <param name="genus"
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35 type="text"
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36 label="Genus"
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37 help="e.g.: Homo" />
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38
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39 <param name="species"
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40 argument="--species"
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41 type="text"
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42 label="Species"
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43 help="e.g.: sapiens" />
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44
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45 <param name="abbr"
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46 type="text"
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47 label="Abbreviation"
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48 help="e.g.: H. sapiens" />
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49
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50 <param name="common"
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51 type="text"
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52 label="Common name"
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53 help="e.g.: Human" />
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54
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55 <param name="description"
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56 argument="--comment"
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57 type="text"
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58 label="Description"
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59 optional="True">
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60 <expand macro="sanitized"/>
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61 </param>
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62
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63 <conditional name="infra">
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64 <param name="use_infra" type="boolean" checked="false" label="Specify an infraspecific rank" />
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65 <when value="false"></when>
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66 <when value="true">
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67 <param name="rank"
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68 argument="--infraspecific_rank"
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69 type="select"
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70 label="Infraspecific Rank">
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71 <option value="subspecies">subspecies</option>
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72 <option value="varietas">varietas</option>
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73 <option value="subvariety">subvariety</option>
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74 <option value="forma">forma</option>
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75 <option value="subforma">subforma</option>
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76 </param>
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77 <param name="name"
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78 argument="--infraspecific_name"
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79 type="text"
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80 label="Infraspecific Name"
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81 help="The infraspecific name of the new organism (e.g. a strain name)" />
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82 </when>
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83 </conditional>
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84 </inputs>
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85 <outputs>
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86 <data format="json" name="results" label="New Tripal organism" />
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87 </outputs>
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88 <tests>
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89 <test expect_failure="true">
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90 <param name="genus" value="Testus" />
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91 <param name="species" value="testum" />
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92 <param name="abbr" value="test" />
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93 <param name="common" value="test stuff" />
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94 <param name="common" value="My cool new test organism" />
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95
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96 <expand macro="test_result" />
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97 </test>
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98 <test expect_failure="true">
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99 <param name="genus" value="Testus" />
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100 <param name="species" value="testum" />
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101 <param name="abbr" value="test" />
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102 <param name="common" value="test stuff" />
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103 <param name="common" value="My cool new test organism" />
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104 <conditional name="infra">
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105 <param name="use_infra" value="True" />
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106 <param name="rank" value="subspecies" />
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107 <param name="name" value="strain3" />
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108 </conditional>
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109
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110 <expand macro="test_result" />
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111 </test>
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112 </tests>
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113 <help><![CDATA[
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114 @HELP_OVERVIEW@
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115
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116 **Create Organism**
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117
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118 With this tool, you can create a new organism in the Tripal/Chado database
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119
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120 @HELP@
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121 ]]></help>
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122 <expand macro="citation"/>
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123 </tool>