Mercurial > repos > iuc > data_manager_semibin

annotate data_manager/data_manager_semibin.xml @ 1:d584aacd7d13 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/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
author iuc
date Fri, 01 Aug 2025 21:25:02 +0000
parents 676915c44e1e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
1 <tool id="data_manager_semibin" name="Download reference genomes (GTDB) for SemiBin" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
2 <description></description>
1
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
3 <macros>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">2.0.2</token>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
6 <token name="@PROFILE@">24.0</token>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
7 </macros>
0
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
8 <requirements>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
10 </requirements>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
1
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
12 mkdir -p '${out_file.extra_files_path}' &&
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
13 #if $type == "test"
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
14 touch '${out_file.extra_files_path}'/empty
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
15 #else
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
16 SemiBin download_GTDB --reference-db-data-dir '${out_file.extra_files_path}'
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
17 #end if
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
18 && cp '$dmjson' '$out_file'
0
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
19 ]]></command>
1
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
20 <configfiles>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
21 <configfile name="dmjson"><![CDATA[#slurp
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
22 #from datetime import datetime
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
23 #set value=datetime.now().strftime("%d%m%Y")
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
24 {
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
25 "data_tables":{
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
26 "gtdb":[
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
27 {
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
28 "value": "$value",
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
29 #if $type == "test"
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
30 "name": "Test",
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
31 "dbkey": "test",
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
32 #else
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
33 "name": "GTDB reference genome generated by MMseqs2 used in SemiBin",
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
34 "dbkey": "gtdb",
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
35 #end if
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
36 "path": "$out_file.extra_files_path"
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
37 }
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
38 ]
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
39 }
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
40 }
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
41 ]]></configfile>
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
42 </configfiles>
0
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
43 <inputs>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
44 <param name="type" type="hidden" value="" />
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
45 </inputs>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
46 <outputs>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
47 <data name="out_file" format="data_manager_json"/>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
48 </outputs>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
49 <tests>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
50 <test expect_num_outputs="1">
1
d584aacd7d13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit 8672b5bdf2029b392cb26d1e426b536e9541b932
iuc
parents: 0
diff changeset
51 <param name="type" value="test" />
0
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
52 <output name="out_file">
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
53 <assert_contents>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
54 <has_text text="test"/>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
55 <has_text text="Test"/>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
56 </assert_contents>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
57 </output>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
58 </test>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
59 </tests>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
60 <help><![CDATA[
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
61 This tool downloads reference genomes (GTDB) for SemiBin
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
62 ]]></help>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
63 <citations>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
64 <citation type="doi">10.1038/s41467-022-29843-y</citation>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
65 </citations>
676915c44e1e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
66 </tool>