Mercurial > repos > gga > tripal_organism_add_organism

comparison organism_add_organism.xml @ 0:56390a41953e 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 05:53:37 -0400
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children 92407294b12e
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-1:000000000000 0:56390a41953e
1 <?xml version="1.0"?>
2 <tool id="organism_add_organism" profile="16.04" name="Create an organism" version="@WRAPPER_VERSION@.0">
3 <description>in Tripal</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package" version="1.5">jq</requirement>
9 </expand>
10 <expand macro="stdio"/>
11 <command><![CDATA[
12
13 @AUTH@
14
15 tripaille organism add_organism
16
17 #if str($species):
18 --species '$species'
19 #end if
20
21 #if str($description):
22 --comment '$description'
23 #end if
24
25 #if $infra.use_infra:
26 --infraspecific_rank '$infra.rank'
27 --infraspecific_name '$infra.name'
28 #end if
29
30 '$genus'
31 '$common'
32 '$abbr'
33
34 | jq -S . > $results
35 ]]></command>
36 <inputs>
37 <param name="genus"
38 type="text"
39 label="Genus"
40 help="e.g.: Homo" />
41
42 <param name="species"
43 argument="--species"
44 type="text"
45 label="Species"
46 optional="True"
47 help="e.g.: sapiens" />
48
49 <param name="abbr"
50 type="text"
51 label="Abbreviation"
52 help="e.g.: H. sapiens" />
53
54 <param name="common"
55 type="text"
56 label="Common name"
57 help="e.g.: Human" />
58
59 <param name="description"
60 argument="--comment"
61 type="text"
62 label="Description"
63 optional="True">
64 <expand macro="sanitized"/>
65 </param>
66
67 <conditional name="infra">
68 <param name="use_infra" type="boolean" checked="false" label="Specify an infraspecific rank" />
69 <when value="false"></when>
70 <when value="true">
71 <param name="rank"
72 argument="--infraspecific_rank"
73 type="select"
74 label="Infraspecific Rank">
75 <option value="subspecies">subspecies</option>
76 <option value="varietas">varietas</option>
77 <option value="subvariety">subvariety</option>
78 <option value="forma">forma</option>
79 <option value="subforma">subforma</option>
80 </param>
81 <param name="name"
82 argument="--infraspecific_name"
83 type="text"
84 label="Infraspecific Name"
85 help="The infraspecific name of the new organism (e.g. a strain name)" />
86 </when>
87 </conditional>
88 </inputs>
89 <outputs>
90 <data format="json" name="results" label="New Tripal organism" />
91 </outputs>
92 <tests>
93 <test expect_failure="true">
94 <param name="genus" value="Testus" />
95 <param name="species" value="testum" />
96 <param name="abbr" value="test" />
97 <param name="common" value="test stuff" />
98 <param name="common" value="My cool new test organism" />
99
100 <expand macro="test_result" />
101 </test>
102 <test expect_failure="true">
103 <param name="genus" value="Testus" />
104 <param name="species" value="testum" />
105 <param name="abbr" value="test" />
106 <param name="common" value="test stuff" />
107 <param name="common" value="My cool new test organism" />
108 <conditional name="infra">
109 <param name="use_infra" value="True" />
110 <param name="rank" value="subspecies" />
111 <param name="name" value="strain3" />
112 </conditional>
113
114 <expand macro="test_result" />
115 </test>
116 </tests>
117 <help><![CDATA[
118 @HELP_OVERVIEW@
119
120 **Create Organism**
121
122 With this tool, you can create a new organism in the Tripal/Chado database
123
124 @HELP@
125 ]]></help>
126 <expand macro="citation"/>
127 </tool>