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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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fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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1 <macros>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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2 <xml name="requirements">
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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3 <requirements>
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4 <requirement type="package" version="@TOOL_VERSION@">vgp-processcuration</requirement>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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5 <yield/>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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6 </requirements>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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7 </xml>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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8 <token name="@TOOL_VERSION@">1.0</token>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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9 <token name="@PROFILE@">21.09</token>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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10 <xml name="edam_ontology">
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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11 <edam_topics>
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12 <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
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13 <edam_topic>topic_3797</edam_topic> <!-- Genome assembly -->
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14 </edam_topics>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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15 </xml>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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16 <xml name="xrefs">
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17 <xrefs>
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18 <xref type="bio.tools">vgp-processcuration</xref>
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19 </xrefs>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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20 </xml>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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21 <xml name="citations">
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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22 <citations>
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23 <citation type="bibtex">
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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24 @misc{vgl_curation,
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25 author = {VGL-Hub},
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26 title = {VGL Curation - ProcessCuration toolkit for genome assembly submission},
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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27 year = {2025},
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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28 url = {https://github.com/vgl-hub/vgl-curation},
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29 }
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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30 </citation>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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31 </citations>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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32 </xml>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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33 <xml name="help_common">
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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34 <![CDATA[
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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35 **About ProcessCuration**
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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36
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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37 ProcessCuration is a Python-based toolkit designed to process manually curated genome assemblies for submission.
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38 It reconciles AGP files (A Golden Path) created in PretextView with genome assembly FASTAs, preparing them for
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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39 database submission through renaming, reorienting, and sorting operations.
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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40
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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41 The toolkit is part of the VGP (Vertebrate Genomes Project) curation pipeline and works in conjunction with
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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42 tools like gfastats and MashMap.
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43
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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44 **Input Naming Convention**
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45
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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46 Scaffolds must follow the naming pattern before curation:
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47 - Haplotype 1: H1.scaffold_X
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48 - Haplotype 2: H2.scaffold_X
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49
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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50 **More Information**
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51
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52 - GitHub repository: https://github.com/vgl-hub/vgl-curation
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53 - VGP Genome Assembly Pipeline: https://vertebrategenomesproject.org/
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54 ]]>
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55 </xml>
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56 </macros>