Mercurial > repos > iuc > vgp_chromosome_assignment

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author iuc
date Wed, 07 Jan 2026 12:48:42 +0000
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1 <tool id="vgp_chromosome_assignment" name="VGP Chromosome Assignment" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Assign chromosome names to scaffolds</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## Create output directory
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10 mkdir -p output_dir &&
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11
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12 ## Run chromosome_assignment
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13 chromosome_assignment
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14 -a '$agp'
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15 -f '$fasta'
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16 -o output_dir
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17
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18 ]]></command>
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19 <inputs>
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20 <param name="agp" type="data" format="tabular" label="Haplotype AGP file"
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21 help="Input haplotype AGP file without haplotig duplications." />
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22 <param name="fasta" type="data" format="fasta" label="Sorted FASTA file"
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23 help="Input sorted FASTA file." />
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24 </inputs>
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25 <outputs>
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26 <data name="inter_chr" format="tabular" from_work_dir="output_dir/inter_chr.tsv"
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27 label="${tool.name} on ${on_string}: Chromosome Mapping Table"/>
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28 <data name="chr_level_fasta" format="fasta" from_work_dir="output_dir/hap.chr_level.fa"
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29 label="${tool.name} on ${on_string}: Chromosome-level FASTA"/>
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30 </outputs>
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31 <tests>
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32 <test expect_num_outputs="2">
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33 <param name="agp" value="test_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
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34 <param name="fasta" value="test_hap1_sorted.fa" ftype="fasta"/>
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35 <output name="inter_chr" file="expected_hap1_inter_chr.tsv" ftype="tabular"/>
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36 <output name="chr_level_fasta" file="expected_hap1_chr_level.fa" ftype="fasta"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 **What it does**
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41
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42 chromosome_assignment substitutes scaffold identifiers with chromosome assignments, generating chromosome-level
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43 sequences and mapping tables.
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44
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45 The tool processes AGP metadata to:
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46
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47 1. Identify sex chromosomes (X, Y, W, Z) and regular chromosomes
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48 2. Filter autosomal scaffolds and assign sequential ``SUPER_`` identifiers
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49 3. Rename sex-linked scaffolds with ``SUPER_X/Y/W/Z`` prefixes
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50 4. Handle unlocalized contigs by replacing parent scaffold names with chromosomal assignments
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51 5. Generate documentation mapping original names to new names
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52
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53 **Inputs**
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54
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55 - **Haplotype AGP file**: Tab-delimited AGP file with chromosome assignment metadata (typically hap.unlocs.no_hapdups.agp from split_agp)
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56 - **Sorted FASTA file**: Sorted sequence file containing scaffolds/contigs (typically sorted using gfastats)
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57
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58 **Outputs**
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59
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60 - **Chromosome Mapping Table (inter_chr.tsv)**: Tab-separated file documenting all scaffold-to-chromosome name transformations
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61 - **Chromosome-level FASTA**: FASTA file with sequences renamed to chromosome-level assignments
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62
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63 **Workflow Context**
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64
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65 This tool is typically run twice in the VGP curation pipeline, once for each haplotype:
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66
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67 1. Run on Haplotype 1: Use Hap1 AGP and Hap1 sorted FASTA
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68 2. Run on Haplotype 2: Use Hap2 AGP and Hap2 sorted FASTA
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70 **Input Preparation**
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72 Before running this tool:
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73
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74 1. Run split_agp to split haplotypes and correct AGP files
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75 2. Use gfastats to sort each haplotype with its corresponding AGP file:
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76 - gfastats hap1.fa -a hap1_unlocs_no_hapdups.agp -o hap1.sorted.fa
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77 - gfastats hap2.fa -a hap2_unlocs_no_hapdups.agp -o hap2.sorted.fa
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78
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79 **Next Steps**
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81 After running chromosome_assignment on both haplotypes:
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82
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83 1. Run MashMap to align the two chromosome-level haplotypes
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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84 2. Use sak_generation with the two inter_chr.tsv files and MashMap output to generate SAK instructions
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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85
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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86 .. class:: infomark
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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87
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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88 **More Information**
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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89
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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90 This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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91
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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92 <expand macro="help_common"/>
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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93 ]]></help>
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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94 <expand macro="citations"/>
9b52f4e2093b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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95 </tool>