Mercurial > repos > iuc > vgp_split_agp

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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 <tool id="vgp_split_agp" name="VGP Split AGP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Correct AGP files and split haplotypes</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 split_agp
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10 -f '$fasta'
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11 -a '$agp'
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12 -o './'
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13 ]]></command>
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14 <inputs>
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15 <param name="fasta" type="data" format="fasta,fasta.gz" label="Assembly FASTA file"
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16 help="Input assembly FASTA file containing both haplotypes." />
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17 <param name="agp" type="data" format="tabular" label="Curated AGP file"
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18 help="Input curated AGP file created in PretextView with haplotype markers (Hap_1/H1 and Hap_2/H2)." />
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19 </inputs>
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20 <outputs>
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21 <data name="corrected_agp" format="tabular" from_work_dir="corrected.agp"
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22 label="${tool.name} on ${on_string}: Corrected AGP"/>
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23
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24 <!-- Haplotype 1 outputs -->
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25 <data name="hap1_agp" format="tabular" from_work_dir="Hap_1/hap1.agp" label="${tool.name} on ${on_string}: Hap1 AGP"/>
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26 <data name="hap1_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_1/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap1 Unlocs without haplotig AGP"/>
fc30c955f2ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
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27 <data name="hap1_haplotigs" format="tabular" from_work_dir="Hap_1/haplotigs.agp" label="${tool.name} on ${on_string}: Hap1 Haplotigs AGP"/>
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28
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29 <!-- Haplotype 2 outputs -->
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30 <data name="hap2_agp" format="tabular" from_work_dir="Hap_2/hap2.agp" label="${tool.name} on ${on_string}: Hap2 AGP"/>
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31 <data name="hap2_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_2/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap2 Unlocs without haplotigs AGP"/>
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32 <data name="hap2_haplotigs" format="tabular" from_work_dir="Hap_2/haplotigs.agp" label="${tool.name} on ${on_string}: Hap2 Haplotigs AGP"/>
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33 </outputs>
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34 <tests>
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35 <test expect_num_outputs="7">
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36 <param name="fasta" value="test_input.fasta.gz" ftype="fasta.gz"/>
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37 <param name="agp" value="test_input.agp" ftype="tabular"/>
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38 <output name="corrected_agp" file="expected_corrected.agp" ftype="tabular"/>
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39 <output name="hap1_agp" file="expected_hap1.agp" ftype="tabular"/>
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40 <output name="hap1_unlocs_no_hapdups" file="expected_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
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41 <output name="hap1_haplotigs" file="expected_hap1_haplotigs.agp" ftype="tabular"/>
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42 <output name="hap2_agp" file="expected_hap2.agp" ftype="tabular"/>
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43 <output name="hap2_unlocs_no_hapdups" file="expected_hap2_unlocs_no_hapdups.agp" ftype="tabular"/>
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44 <output name="hap2_haplotigs" file="expected_hap2_haplotigs.agp" ftype="tabular"/>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 **What it does**
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49
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50 split_agp corrects AGP files for sequence length discrepancies, splits haplotypes into separate files,
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51 assigns unlocalized sequences, and removes haplotig duplications.
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52
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53 This tool performs three sequential operations:
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54
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55 1. **AGPcorrect**: Validates sequence lengths from FASTA against AGP coordinates, adjusting start/end positions
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56 2. **hap_split**: Segregates lines containing haplotype markers into separate directories (Hap_1 and Hap_2)
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57 3. **unloc**: Processes metadata tags, renames unloc scaffolds with sequential numbering, removes haplotigs
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58
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59 **Inputs**
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60
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61 - **Assembly FASTA file**: FASTA file containing both haplotypes (may be gzip-compressed)
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62 - **Curated AGP file**: Tab-delimited AGP file with haplotype markers (Hap_1/H1 or Hap_2/H2)
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63
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64 **Outputs**
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65
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66 - **Corrected AGP**: Length-validated AGP file with corrected coordinates
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67 - **Hap1 AGP**: Haplotype 1 AGP file
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68 - **Hap1 Unlocs No Hapdups**: Haplotype 1 AGP with unlocalized sequences assigned and haplotigs removed
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69 - **Hap1 Haplotigs**: Removed duplicate haplotigs from Haplotype 1
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70 - **Hap2 AGP**: Haplotype 2 AGP file
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71 - **Hap2 Unlocs No Hapdups**: Haplotype 2 AGP with unlocalized sequences assigned and haplotigs removed
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72 - **Hap2 Haplotigs**: Removed duplicate haplotigs from Haplotype 2
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73
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74 **Input Naming Requirements**
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75
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76 ⚠️ **Important**: Scaffolds in the input FASTA must follow this naming convention:
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77 - Haplotype 1: H1.scaffold_X
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78 - Haplotype 2: H2.scaffold_X
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79
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80 This naming pattern is required before manual curation in PretextView.
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81
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82 **Next Steps**
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83
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84 After running split_agp, use the gfastats tool to sort each haplotype:
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85
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86 1. Sort Haplotype 1: gfastats with Hap1 Unlocs No Hapdups AGP
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87 2. Sort Haplotype 2: gfastats with Hap2 Unlocs No Hapdups AGP
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88
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89 Then proceed to the chromosome_assignment tool to assign chromosome-level names.
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90
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91 .. class:: infomark
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92
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93 **More Information**
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94
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95 This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.
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96
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97 <expand macro="help_common"/>
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>