Mercurial > repos > iuc > data_manager_funannotate

comparison data_manager/funannotate.xml @ 4:1c81a82b5b8e draft

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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 22:33:21 +0000
parents 0cadd0a04412
children
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3:0cadd0a04412 4:1c81a82b5b8e
1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01"> 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>
2 <requirements> 6 <requirements>
3 <requirement type="package" version="1.8.9">funannotate</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
4 <requirement type="package" version="2.26.0">requests</requirement>
5 </requirements> 8 </requirements>
6 <version_command>funannotate check --show-versions</version_command> 9 <version_command>funannotate check --show-versions</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
8 #if $wget: 11 #if $wget:
9 ## Asked for wget, we assume there's a certificate problem on (at least) one 12 ## Asked for wget, we assume there's a certificate problem on (at least) one
10 ## of the many requested servers, force disable of all checks 13 ## of the many requested servers, force disable of all checks
11 echo "check_certificate = off" > \$HOME/.wgetrc && 14 echo "check_certificate = off" > \$HOME/.wgetrc &&
12 #end if 15 #end if
13 16
14 python -u '$__tool_directory__/funannotate.py' 17 funannotate setup
15 $partial_data 18 -d '$output_file.extra_files_path'
16 $wget 19 #if $partial_data
17 \$(date +'%Y-%m-%d-%H%M%S') 20 -i merops -b eukaryota
18 'funannotate' 21 #else
19 '${output_file}' 22 -b all
23 #end if
24 $wget
25 &&
26 cp '$dmjson' '$output_file'
20 ]]></command> 27 ]]></command>
28 <configfiles>
29 <configfile name="dmjson"><![CDATA[
30 #from datetime import datetime
31 #set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
32 {
33 "data_tables":{
34 "funannotate":[
35 {
36 "value":"$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>
21 <inputs> 45 <inputs>
22 <param name="partial_data" type="hidden" value="" help="Used for testing"/> 46 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
23 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/> 47 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
24 </inputs> 48 </inputs>
25 <outputs> 49 <outputs>
29 <test> 53 <test>
30 <param name="partial_data" value="--partial"/> 54 <param name="partial_data" value="--partial"/>
31 <output name="output_file"> 55 <output name="output_file">
32 <assert_contents> 56 <assert_contents>
33 <has_text text="Funannotate database "/> 57 <has_text text="Funannotate database "/>
34 <has_text text='"format_version": "1.0"'/> 58 <has_text text='"format_version":"1.0"'/>
35 </assert_contents> 59 </assert_contents>
36 </output> 60 </output>
37 </test> 61 </test>
38 <test> 62 <test>
39 <param name="partial_data" value="--partial"/> 63 <param name="partial_data" value="--partial"/>
40 <param name="wget" value="True"/> 64 <param name="wget" value="True"/>
41 <output name="output_file"> 65 <output name="output_file">
42 <assert_contents> 66 <assert_contents>
43 <has_text text="Funannotate database "/> 67 <has_text text="Funannotate database "/>
44 <has_text text='"format_version": "1.0"'/> 68 <has_text text='"format_version":"1.0"'/>
45 </assert_contents> 69 </assert_contents>
46 </output> 70 </output>
47 </test> 71 </test>
48 </tests> 72 </tests>
49 <help><![CDATA[ 73 <help><![CDATA[