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comparison chromosome_assignment.xml @ 0:9b52f4e2093b draft default tip

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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 12:48:42 +0000
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1 <tool id="vgp_chromosome_assignment" name="VGP Chromosome Assignment" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Assign chromosome names to scaffolds</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ## Create output directory
10 mkdir -p output_dir &&
11
12 ## Run chromosome_assignment
13 chromosome_assignment
14 -a '$agp'
15 -f '$fasta'
16 -o output_dir
17
18 ]]></command>
19 <inputs>
20 <param name="agp" type="data" format="tabular" label="Haplotype AGP file"
21 help="Input haplotype AGP file without haplotig duplications." />
22 <param name="fasta" type="data" format="fasta" label="Sorted FASTA file"
23 help="Input sorted FASTA file." />
24 </inputs>
25 <outputs>
26 <data name="inter_chr" format="tabular" from_work_dir="output_dir/inter_chr.tsv"
27 label="${tool.name} on ${on_string}: Chromosome Mapping Table"/>
28 <data name="chr_level_fasta" format="fasta" from_work_dir="output_dir/hap.chr_level.fa"
29 label="${tool.name} on ${on_string}: Chromosome-level FASTA"/>
30 </outputs>
31 <tests>
32 <test expect_num_outputs="2">
33 <param name="agp" value="test_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
34 <param name="fasta" value="test_hap1_sorted.fa" ftype="fasta"/>
35 <output name="inter_chr" file="expected_hap1_inter_chr.tsv" ftype="tabular"/>
36 <output name="chr_level_fasta" file="expected_hap1_chr_level.fa" ftype="fasta"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 **What it does**
41
42 chromosome_assignment substitutes scaffold identifiers with chromosome assignments, generating chromosome-level
43 sequences and mapping tables.
44
45 The tool processes AGP metadata to:
46
47 1. Identify sex chromosomes (X, Y, W, Z) and regular chromosomes
48 2. Filter autosomal scaffolds and assign sequential ``SUPER_`` identifiers
49 3. Rename sex-linked scaffolds with ``SUPER_X/Y/W/Z`` prefixes
50 4. Handle unlocalized contigs by replacing parent scaffold names with chromosomal assignments
51 5. Generate documentation mapping original names to new names
52
53 **Inputs**
54
55 - **Haplotype AGP file**: Tab-delimited AGP file with chromosome assignment metadata (typically hap.unlocs.no_hapdups.agp from split_agp)
56 - **Sorted FASTA file**: Sorted sequence file containing scaffolds/contigs (typically sorted using gfastats)
57
58 **Outputs**
59
60 - **Chromosome Mapping Table (inter_chr.tsv)**: Tab-separated file documenting all scaffold-to-chromosome name transformations
61 - **Chromosome-level FASTA**: FASTA file with sequences renamed to chromosome-level assignments
62
63 **Workflow Context**
64
65 This tool is typically run twice in the VGP curation pipeline, once for each haplotype:
66
67 1. Run on Haplotype 1: Use Hap1 AGP and Hap1 sorted FASTA
68 2. Run on Haplotype 2: Use Hap2 AGP and Hap2 sorted FASTA
69
70 **Input Preparation**
71
72 Before running this tool:
73
74 1. Run split_agp to split haplotypes and correct AGP files
75 2. Use gfastats to sort each haplotype with its corresponding AGP file:
76 - gfastats hap1.fa -a hap1_unlocs_no_hapdups.agp -o hap1.sorted.fa
77 - gfastats hap2.fa -a hap2_unlocs_no_hapdups.agp -o hap2.sorted.fa
78
79 **Next Steps**
80
81 After running chromosome_assignment on both haplotypes:
82
83 1. Run MashMap to align the two chromosome-level haplotypes
84 2. Use sak_generation with the two inter_chr.tsv files and MashMap output to generate SAK instructions
85
86 .. class:: infomark
87
88 **More Information**
89
90 This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.
91
92 <expand macro="help_common"/>
93 ]]></help>
94 <expand macro="citations"/>
95 </tool>