Mercurial > repos > iuc > data_manager_funannotate

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
children
comparison
equal deleted inserted replaced
4:1c81a82b5b8e 5:5459ec34767a
1 <tool id="data_manager_funannotate_options" name="Funannotate options 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 $test:
12 funannotate setup -d ./test/ -i busco busco_outgroups -b eukaryota > /dev/null &&
13 #set db_path="./test"
14 #else
15 #set db_path=$database.fields.path
16 #end if
17 python '$__tool_directory__/extract.py' '$db_path' '$database' '$output_file'
18 ]]></command>
19 <inputs>
20 <param name="test" type="hidden" value="" help="Used for testing"/>
21 <param name="database" label="Funannotate database" type="select">
22 <options from_data_table="funannotate">
23 <column name="value" index="0" />
24 <column name="name" index="1" />
25 <column name="path" index="3" />
26 <filter type="sort_by" column="0" reverse_sort_order="true"/>
27 <!-- <filter type="static_value" column="2" value="1.0" /> -->
28 </options>
29 </param>
30 </inputs>
31 <outputs>
32 <data name="output_file" format="data_manager_json"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="test" value="true"/>
37 <param name="database" value="test"/>
38 <output name="output_file">
39 <assert_contents>
40 <has_text text="busco_db" n="1"/>
41 <has_text text="outgroup" n="6"/>
42 <has_text text="trained_species" n="166"/>
43 </assert_contents>
44 </output>
45 <assert_stdout>
46 <has_line line="1 x busco_db"/>
47 <has_line line="166 x trained_species"/>
48 <has_line line="6 x outgroup"/>
49 </assert_stdout>
50 </test>
51 </tests>
52 <help><![CDATA[
53 This data managers determines the options available in the select parameters of the funannotate tool
54 for a given funannotate DB in the funannotate data table
55
56 .. _funannotate: https://funannotate.readthedocs.io
57 ]]></help>
58 <citations>
59 <citation type="doi">10.5281/zenodo.4054262</citation>
60 </citations>
61 </tool>