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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/dotprep commit 6db87bb19217d256b13cd66810043b667d1c7638
author bgruening
date Wed, 03 Dec 2025 16:17:07 +0000
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1 <tool id="dotprep" name="dotPrep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>Apply unique anchor filtering and prepare Dot coordinates</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">25.0</token>
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7 </macros>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$delta' input.delta.gz &&
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10 python3 '$__tool_directory__/dotPrep.py'
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11 --delta input.delta.gz
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12 --out result
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13 --unique-length $unique_length
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14 --overview $overview
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15 ]]></command>
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16 <inputs>
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17 <param name="delta" type="data" format="tabular" label="Delta file" help="Input delta file from alignment tool (e.g., MUMmer)"/>
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18 <param name="unique_length" type="integer" value="10000" min="0" label="Unique sequence length threshold" help="The total length of unique sequence an alignment must have on the query side to be retained"/>
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19 <param name="overview" type="integer" value="1000" min="1" label="Number of alignments for overview" help="The number of alignments to include in the coords.idx output file for Dot overview"/>
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20 </inputs>
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21 <outputs>
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22 <data name="result" format="tabular" label="${tool.name} on ${on_string}: Output delta file" from_work_dir="result.uniqueAnchorFiltered*"/>
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23 <data name="coords" format="tabular" label="${tool.name} on ${on_string}: filtered coords" from_work_dir="result.coords"/>
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24 <data name="coords_idx" format="tabular" label="${tool.name} on ${on_string}: coords.idx" from_work_dir="result.coords.idx"/>
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25 </outputs>
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26 <tests>
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27 <test expect_num_outputs="3">
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28 <param name="delta" location="https://zenodo.org/records/17592326/files/input.res.uniqueAnchorFiltered_l10000.delta.gz"/>
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29 <param name="unique_length" value="10000"/>
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30 <param name="overview" value="1000"/>
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31 <output name="result" location="https://zenodo.org/records/17592326/files/test_output.delta.gz" compare="sim_size"/>
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32 <output name="coords" ftype="tabular">
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33 <assert_contents>
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34 <has_n_lines n="21848"/>
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35 <has_line line="28999,29316,9912,10233,h1tg000718l"/>
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36 <has_line line="32087,32264,16943,17122,h1tg000718l"/>
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37 <has_line line="41139,41490,26157,26508,h1tg000718l"/>
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38 </assert_contents>
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39 </output>
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40 <output name="coords_idx" ftype="tabular">
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41 <assert_contents>
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42 <has_n_lines n="1840"/>
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43 </assert_contents>
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44 </output>
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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 This tool takes a delta file from genome alignment tools (such as MUMmer's nucmer), applies unique anchor filtering, and prepares coordinate input files for visualization with Dot.
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51
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52 **Inputs**
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53
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54 - **Delta file**: Output from alignment programs like MUMmer's nucmer
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55 - **Unique sequence length threshold**: Minimum total length of unique sequence an alignment must have on the query side to be retained (Default: 10000 bp)
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56 - **Number of alignments for overview**: Number of top alignments to include in the coords.idx file for Dot overview visualization (Default: 1000)
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57
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58 **Outputs**
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59
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60 - **Filtered coords file**: Coordinate file with unique anchor filtering applied
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61 - **coords.idx file**: Index file containing top alignments for Dot visualization overview
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62
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63 **About Unique Anchor Filtering**
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64
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65 The unique anchor filtering strategy identifies high-quality alignments by requiring a minimum amount of unique sequence. This helps filter out repetitive regions and focus on reliable anchoring points between sequences.
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66
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67 **Aknowledgements**
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68
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69 dotPrep is part of Assemblytics, developed by Maria Nattestad. For more information, please visit the [Assemblytics GitHub repository](https://github.com/MariaNattestad/dot/tree/master)
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70
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71 ]]></help>
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72 <citations>
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73 <citation type="bibtex">
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74 @misc{githubdotprep,
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75 author = {MariaNattestad},
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76 year = {2023},
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77 title = {dotPrep},
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78 publisher = {GitHub},
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79 journal = {GitHub repository},
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80 url = {https://github.com/MariaNattestad/dot/blob/master/DotPrep.py},
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81 }</citation>
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82 </citations>
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83 <creator>
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84 <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
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85 <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
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86 </creator>
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87 </tool>