Mercurial > repos > iuc > vgp_split_agp
diff macros.xml @ 0:fc30c955f2ac draft default tip
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jan 07 12:48:27 2026 +0000 @@ -0,0 +1,56 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">vgp-processcuration</requirement> + <yield/> + </requirements> + </xml> + <token name="@TOOL_VERSION@">1.0</token> + <token name="@PROFILE@">21.09</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0622</edam_topic> <!-- Genomics --> + <edam_topic>topic_3797</edam_topic> <!-- Genome assembly --> + </edam_topics> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">vgp-processcuration</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> +@misc{vgl_curation, + author = {VGL-Hub}, + title = {VGL Curation - ProcessCuration toolkit for genome assembly submission}, + year = {2025}, + url = {https://github.com/vgl-hub/vgl-curation}, +} + </citation> + </citations> + </xml> + <xml name="help_common"> + <![CDATA[ +**About ProcessCuration** + +ProcessCuration is a Python-based toolkit designed to process manually curated genome assemblies for submission. +It reconciles AGP files (A Golden Path) created in PretextView with genome assembly FASTAs, preparing them for +database submission through renaming, reorienting, and sorting operations. + +The toolkit is part of the VGP (Vertebrate Genomes Project) curation pipeline and works in conjunction with +tools like gfastats and MashMap. + +**Input Naming Convention** + +Scaffolds must follow the naming pattern before curation: +- Haplotype 1: H1.scaffold_X +- Haplotype 2: H2.scaffold_X + +**More Information** + +- GitHub repository: https://github.com/vgl-hub/vgl-curation +- VGP Genome Assembly Pipeline: https://vertebrategenomesproject.org/ + ]]> + </xml> +</macros>
