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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
author iuc
date Wed, 07 Jan 2026 12:48:27 +0000
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1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">vgp-processcuration</requirement>
5 <yield/>
6 </requirements>
7 </xml>
8 <token name="@TOOL_VERSION@">1.0</token>
9 <token name="@PROFILE@">21.09</token>
10 <xml name="edam_ontology">
11 <edam_topics>
12 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
13 <edam_topic>topic_3797</edam_topic> <!-- Genome assembly -->
14 </edam_topics>
15 </xml>
16 <xml name="xrefs">
17 <xrefs>
18 <xref type="bio.tools">vgp-processcuration</xref>
19 </xrefs>
20 </xml>
21 <xml name="citations">
22 <citations>
23 <citation type="bibtex">
24 @misc{vgl_curation,
25 author = {VGL-Hub},
26 title = {VGL Curation - ProcessCuration toolkit for genome assembly submission},
27 year = {2025},
28 url = {https://github.com/vgl-hub/vgl-curation},
29 }
30 </citation>
31 </citations>
32 </xml>
33 <xml name="help_common">
34 <![CDATA[
35 **About ProcessCuration**
36
37 ProcessCuration is a Python-based toolkit designed to process manually curated genome assemblies for submission.
38 It reconciles AGP files (A Golden Path) created in PretextView with genome assembly FASTAs, preparing them for
39 database submission through renaming, reorienting, and sorting operations.
40
41 The toolkit is part of the VGP (Vertebrate Genomes Project) curation pipeline and works in conjunction with
42 tools like gfastats and MashMap.
43
44 **Input Naming Convention**
45
46 Scaffolds must follow the naming pattern before curation:
47 - Haplotype 1: H1.scaffold_X
48 - Haplotype 2: H2.scaffold_X
49
50 **More Information**
51
52 - GitHub repository: https://github.com/vgl-hub/vgl-curation
53 - VGP Genome Assembly Pipeline: https://vertebrategenomesproject.org/
54 ]]>
55 </xml>
56 </macros>