Mercurial > repos > iuc > data_manager_funannotate

comparison data_manager/funannotate.xml @ 5:5459ec34767a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author iuc
date Fri, 07 Mar 2025 22:33:29 +0000
parents 1c81a82b5b8e
children
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4:1c81a82b5b8e 5:5459ec34767a
1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
2 <macros>
3 <token name="@TOOL_VERSION@">1.8.15</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
8 </requirements>
9 <version_command>funannotate check --show-versions</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $wget:
12 ## Asked for wget, we assume there's a certificate problem on (at least) one
13 ## of the many requested servers, force disable of all checks
14 echo "check_certificate = off" > \$HOME/.wgetrc &&
15 #end if
16
17 funannotate setup
18 -d '$output_file.extra_files_path'
19 #if $partial_data
20 -i merops -b eukaryota
21 #else
22 -b all
23 #end if
24 $wget
25 &&
26 cp '$dmjson' '$output_file'
27 ]]></command>
28 <configfiles>
29 <configfile name="dmjson"><![CDATA[
30 #from datetime import datetime
31 #set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
32 {
33 "data_tables":{
34 "funannotate":[
35 {
36 "value":"$version_id",
37 "description":"Funannotate database $version_id",
38 "format_version":"1.0",
39 "path":"$output_file.extra_files_path"
40 }
41 ]
42 }
43 }]]></configfile>
44 </configfiles>
45 <inputs>
46 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
47 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
48 </inputs>
49 <outputs>
50 <data name="output_file" format="data_manager_json"/>
51 </outputs>
52 <tests>
53 <test>
54 <param name="partial_data" value="--partial"/>
55 <output name="output_file">
56 <assert_contents>
57 <has_text text="Funannotate database "/>
58 <has_text text='"format_version":"1.0"'/>
59 </assert_contents>
60 </output>
61 </test>
62 <test>
63 <param name="partial_data" value="--partial"/>
64 <param name="wget" value="True"/>
65 <output name="output_file">
66 <assert_contents>
67 <has_text text="Funannotate database "/>
68 <has_text text='"format_version":"1.0"'/>
69 </assert_contents>
70 </output>
71 </test>
72 </tests>
73 <help><![CDATA[
74 This data managers fetches data from various databases for the funannotate
75 annotation tool and updates the funannotate data table.
76
77 .. _funannotate: https://funannotate.readthedocs.io
78 ]]></help>
79 <citations>
80 <citation type="doi">10.5281/zenodo.4054262</citation>
81 </citations>
82 </tool>