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annotate longdust.xml @ 0:54a33dfe0187 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
author iuc
date Wed, 01 Oct 2025 12:22:23 +0000
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54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
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1 <tool id="longdust" name="longdust" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>Detect low-complexity regions in long sequences</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="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 longdust '$input'
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9 -k $k
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10 -w $w
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11 -t $t
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12 -e $e
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13 $f
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14 $a
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15 > '$output'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="fasta,fastq.gz" label="Input FASTA file"/>
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19 <param argument="-k" type="integer" label="k-mer length" value="7" help="k-mer length"/>
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20 <param argument="-w" type="integer" label="Window size" value="5000" help="Window size"/>
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21 <param argument="-t" type="float" label="Score threshold" value="0.6" help="Score threshold"/>
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22 <param argument="-e" type="integer" label="Extension X-drop length" value="50" help="Extension X-drop length (0 to disable)"/>
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23 <param argument="-f" type="boolean" label="Forward strand only" truevalue="-f" falsevalue="" checked="false" help="Limit analysis to forward strand only" />
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24 <param argument="-a" type="boolean" label="Enable Guaranteed O(Lw) Algorithm" truevalue="-a" falsevalue="" checked="false" help="Use the guaranteed O(Lw) algorithm with increased approximation for faster runtime on large genomes. This mode evaluates only the smallest candidate start per position, reducing runtime to a strict O(Lw) but may miss ~5-10% of low-complexity regions compared to the default."/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="bed"/>
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28 </outputs>
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29 <tests>
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30 <test expect_num_outputs="1">
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31 <param name="input" location="https://zenodo.org/records/17226147/files/GCF_000146045.2_R64_genomic.fna.gz"/>
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32 <param name="k" value="6"/>
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33 <param name="w" value="1000"/>
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34 <param name="t" value="0.55"/>
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35 <param name="e" value="0"/>
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36 <param name="f" value="false"/>
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37 <param name="a" value="false"/>
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38 <output name="output" ftype="bed">
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39 <assert_contents>
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40 <has_n_columns n="3"/>
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41 <has_n_lines n="7426"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47
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48 .. class:: infomark
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49
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50 **What it does**
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51
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52 *longdust* detects low-complexity (dusty) regions in long DNA sequences. It scans input FASTA sequences using k-mer statistics and reports regions that fall below a complexity threshold.
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53 These regions are often repetitive or homopolymeric stretches that may interfere with sequence analysis, alignment, or downstream bioinformatics pipelines.
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54
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55 The method is tunable via parameters for k-mer size, window size, score threshold, and extension length, allowing you to control how strict or relaxed the detection should be.
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56
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57
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58 **Input**
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59 - A FASTA file containing DNA sequences (typically long reads or assembled contigs).
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60 - Optional parameters to configure detection:
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61
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62 - **-k** : k-mer length (default 7)
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63 - **-w** : window size (default 5000)
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64 - **-t** : score threshold (default 0.6)
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65 - **-e** : extension X-drop length, 0 disables extension (default 50)
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66 - **-f** : forward strand only (optional flag)
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67 - **-a** : approximate O(Lw) algorithm (optional flag)
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68
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69 * Recommend w < 4^k for performance, especially given large w
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70 * Use "-k6 -w1000 -t.55" for more relaxed but shorter regions
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71
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72 **Output**
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73
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74 - A BED file listing detected low-complexity regions
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75
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76 ]]></help>
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77 <expand macro="citations"/>
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78 <expand macro="creator"/>
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79 </tool>