Mercurial > repos > gga > tripal_organism_get_organisms

comparison organism_get_organisms.xml @ 0:791692de64d6 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 05:53:54 -0400
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1 <?xml version="1.0"?>
2 <tool id="organism_get_organisms" profile="16.04" name="Get organisms" version="@WRAPPER_VERSION@.0">
3 <description>from 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 get_organisms
16
17 #if $organism_id:
18 --organism_id "$organism_id"
19 #end if
20 #if $genus:
21 --genus "$genus"
22 #end if
23 #if $species:
24 --species "$species"
25 #end if
26 #if $common:
27 --common "$common"
28 #end if
29 #if $abbr:
30 --abbr "$abbr"
31 #end if
32 #if $comment:
33 --comment "$comment"
34 #end if
35
36 | jq -S . > $results
37 ]]></command>
38 <inputs>
39 <param name="organism_id" label="Organism Id" argument="organism_id" type="text" optional="true" help="An organism ID" />
40 <param name="genus" label="Genus" argument="genus" type="text" optional="true" help="The genus of the organism" />
41 <param name="species" label="Species" argument="species" type="text" optional="true" help="The species of the organism" />
42 <param name="common" label="Common" argument="common" type="text" optional="true" help="The common name of the organism" />
43 <param name="abbr" label="Abbr" argument="abbr" type="text" optional="true" help="The abbreviation of the organism" />
44 <param name="comment" label="Comment" argument="comment" type="text" optional="true" help="A comment / description" />
45 </inputs>
46 <outputs>
47 <data format="json" name="results" label="Tripal organisms" />
48 </outputs>
49 <tests>
50 <test expect_failure="true">
51 <expand macro="test_result" />
52 </test>
53 </tests>
54 <help><![CDATA[
55 @HELP_OVERVIEW@
56
57 **Get Organisms**
58
59 With this tool, you can list organisms from the Tripal/Chado database
60
61 @HELP@
62 ]]></help>
63 <expand macro="citation"/>
64 </tool>