Mercurial > repos > iuc > vgp_split_agp

annotate split_agp.xml @ 0:4b67a066df1d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
author iuc
date Wed, 07 Jan 2026 12:47:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
1 <tool id="vgp_split_agp" name="VGP Split AGP" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
2 <description>Correct AGP files and split haplotypes</description>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
3 <macros>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
4 <import>macros.xml</import>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
5 </macros>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
9 split_agp
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
10 -f '$fasta'
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
11 -a '$agp'
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
12 -o './'
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
13 ]]></command>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
14 <inputs>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
15 <param name="fasta" type="data" format="fasta,fasta.gz" label="Assembly FASTA file"
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
16 help="Input assembly FASTA file containing both haplotypes." />
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
17 <param name="agp" type="data" format="tabular" label="Curated AGP file"
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
18 help="Input curated AGP file created in PretextView with haplotype markers (Hap_1/H1 and Hap_2/H2)." />
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
19 </inputs>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
20 <outputs>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
21 <data name="corrected_agp" format="tabular" from_work_dir="corrected.agp"
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
22 label="${tool.name} on ${on_string}: Corrected AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
23
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
24 <!-- Haplotype 1 outputs -->
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
25 <data name="hap1_agp" format="tabular" from_work_dir="Hap_1/hap1.agp" label="${tool.name} on ${on_string}: Hap1 AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
26 <data name="hap1_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_1/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap1 Unlocs without haplotig AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
27 <data name="hap1_haplotigs" format="tabular" from_work_dir="Hap_1/haplotigs.agp" label="${tool.name} on ${on_string}: Hap1 Haplotigs AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
28
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
29 <!-- Haplotype 2 outputs -->
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
30 <data name="hap2_agp" format="tabular" from_work_dir="Hap_2/hap2.agp" label="${tool.name} on ${on_string}: Hap2 AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
31 <data name="hap2_unlocs_no_hapdups" format="tabular" from_work_dir="Hap_2/hap.unlocs.no_hapdups.agp" label="${tool.name} on ${on_string}: Hap2 Unlocs without haplotigs AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
32 <data name="hap2_haplotigs" format="tabular" from_work_dir="Hap_2/haplotigs.agp" label="${tool.name} on ${on_string}: Hap2 Haplotigs AGP"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
33 </outputs>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
34 <tests>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
35 <test expect_num_outputs="7">
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
36 <param name="fasta" value="test_input.fasta.gz" ftype="fasta.gz"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
37 <param name="agp" value="test_input.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
38 <output name="corrected_agp" file="expected_corrected.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
39 <output name="hap1_agp" file="expected_hap1.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
40 <output name="hap1_unlocs_no_hapdups" file="expected_hap1_unlocs_no_hapdups.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
41 <output name="hap1_haplotigs" file="expected_hap1_haplotigs.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
42 <output name="hap2_agp" file="expected_hap2.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
43 <output name="hap2_unlocs_no_hapdups" file="expected_hap2_unlocs_no_hapdups.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
44 <output name="hap2_haplotigs" file="expected_hap2_haplotigs.agp" ftype="tabular"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
45 </test>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
46 </tests>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
47 <help><![CDATA[
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
48 **What it does**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
49
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
50 split_agp corrects AGP files for sequence length discrepancies, splits haplotypes into separate files,
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
51 assigns unlocalized sequences, and removes haplotig duplications.
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
52
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
53 This tool performs three sequential operations:
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
54
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
55 1. **AGPcorrect**: Validates sequence lengths from FASTA against AGP coordinates, adjusting start/end positions
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
56 2. **hap_split**: Segregates lines containing haplotype markers into separate directories (Hap_1 and Hap_2)
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
57 3. **unloc**: Processes metadata tags, renames unloc scaffolds with sequential numbering, removes haplotigs
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
58
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
59 **Inputs**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
60
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
61 - **Assembly FASTA file**: FASTA file containing both haplotypes (may be gzip-compressed)
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
62 - **Curated AGP file**: Tab-delimited AGP file with haplotype markers (Hap_1/H1 or Hap_2/H2)
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
63
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
64 **Outputs**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
65
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
66 - **Corrected AGP**: Length-validated AGP file with corrected coordinates
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
67 - **Hap1 AGP**: Haplotype 1 AGP file
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
68 - **Hap1 Unlocs No Hapdups**: Haplotype 1 AGP with unlocalized sequences assigned and haplotigs removed
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
69 - **Hap1 Haplotigs**: Removed duplicate haplotigs from Haplotype 1
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
70 - **Hap2 AGP**: Haplotype 2 AGP file
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
71 - **Hap2 Unlocs No Hapdups**: Haplotype 2 AGP with unlocalized sequences assigned and haplotigs removed
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
72 - **Hap2 Haplotigs**: Removed duplicate haplotigs from Haplotype 2
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
73
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
74 **Input Naming Requirements**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
75
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
76 ⚠️ **Important**: Scaffolds in the input FASTA must follow this naming convention:
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
77 - Haplotype 1: H1.scaffold_X
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
78 - Haplotype 2: H2.scaffold_X
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
79
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
80 This naming pattern is required before manual curation in PretextView.
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
81
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
82 **Next Steps**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
83
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
84 After running split_agp, use the gfastats tool to sort each haplotype:
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
85
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
86 1. Sort Haplotype 1: gfastats with Hap1 Unlocs No Hapdups AGP
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
87 2. Sort Haplotype 2: gfastats with Hap2 Unlocs No Hapdups AGP
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
88
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
89 Then proceed to the chromosome_assignment tool to assign chromosome-level names.
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
90
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
91 .. class:: infomark
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
92
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
93 **More Information**
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
94
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
95 This tool is part of the VGP ProcessCuration pipeline for preparing curated genome assemblies for submission.
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
96
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
97 <expand macro="help_common"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
98 ]]></help>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
99 <expand macro="citations"/>
4b67a066df1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration commit c25e877636f68656a0005883efb0f03b5ffd6b0c
iuc
parents:
diff changeset
100 </tool>