Mercurial > repos > iuc > longdust

annotate longdust.xml @ 2:5e9dd32b702a 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/longdust commit aa41edcbf8a683b0202d18f9bf906f920370ab7a
author iuc
date Mon, 01 Dec 2025 12:21:21 +0000
parents 9607b6eccee4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
1 <tool id="longdust" name="longdust" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
2 <description>Detect low-complexity regions in long sequences</description>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
3 <macros>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
4 <import>macros.xml</import>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
5 </macros>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
8 longdust '$input'
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
9 -k $k
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
10 -w $w
1
9607b6eccee4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust commit 474cb80dc8dd39926468460d6ece4f37cd01aee3
iuc
parents: 0
diff changeset
11 -g $g
0
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
12 -t $t
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
13 -e $e
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
14 $f
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
15 $a
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
16 > '$output'
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
17 ]]></command>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
18 <inputs>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
19 <param name="input" type="data" format="fasta,fastq.gz" label="Input FASTA file"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
20 <param argument="-k" type="integer" label="k-mer length" value="7" help="k-mer length"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
21 <param argument="-w" type="integer" label="Window size" value="5000" help="Window size"/>
1
9607b6eccee4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust commit 474cb80dc8dd39926468460d6ece4f37cd01aee3
iuc
parents: 0
diff changeset
22 <param argument="-g" type="float" label="Genome-wide GC content" value="0.5" help="Specify genome-wide GC content"/>
0
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
23 <param argument="-t" type="float" label="Score threshold" value="0.6" help="Score threshold"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
24 <param argument="-e" type="integer" label="Extension X-drop length" value="50" help="Extension X-drop length (0 to disable)"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
25 <param argument="-f" type="boolean" label="Forward strand only" truevalue="-f" falsevalue="" checked="false" help="Limit analysis to forward strand only" />
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
26 <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
iuc
parents:
diff changeset
27 </inputs>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
28 <outputs>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
29 <data name="output" format="bed"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
30 </outputs>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
31 <tests>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
32 <test expect_num_outputs="1">
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
33 <param name="input" location="https://zenodo.org/records/17226147/files/GCF_000146045.2_R64_genomic.fna.gz"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
34 <param name="k" value="6"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
35 <param name="w" value="1000"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
36 <param name="t" value="0.55"/>
1
9607b6eccee4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust commit 474cb80dc8dd39926468460d6ece4f37cd01aee3
iuc
parents: 0
diff changeset
37 <param name="g" value="0.5"/>
0
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
38 <param name="e" value="0"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
39 <param name="f" value="false"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
40 <param name="a" value="false"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
41 <output name="output" ftype="bed">
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
42 <assert_contents>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
43 <has_n_columns n="3"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
44 <has_n_lines n="7426"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
45 </assert_contents>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
46 </output>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
47 </test>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
48 </tests>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
49 <help><![CDATA[
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
50
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
51 .. class:: infomark
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
52
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
53 **What it does**
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
54
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
55 *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.
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
56 These regions are often repetitive or homopolymeric stretches that may interfere with sequence analysis, alignment, or downstream bioinformatics pipelines.
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
57
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
58 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.
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
59
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
60
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
61 **Input**
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
62 - A FASTA file containing DNA sequences (typically long reads or assembled contigs).
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
63 - Optional parameters to configure detection:
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
64
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
65 - **-k** : k-mer length (default 7)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
66 - **-w** : window size (default 5000)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
67 - **-t** : score threshold (default 0.6)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
68 - **-e** : extension X-drop length, 0 disables extension (default 50)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
69 - **-f** : forward strand only (optional flag)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
70 - **-a** : approximate O(Lw) algorithm (optional flag)
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
71
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
72 * Recommend w < 4^k for performance, especially given large w
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
73 * Use "-k6 -w1000 -t.55" for more relaxed but shorter regions
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
74
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
75 **Output**
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
76
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
77 - A BED file listing detected low-complexity regions
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
78
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
79 ]]></help>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
80 <expand macro="citations"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
81 <expand macro="creator"/>
54a33dfe0187 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust/ commit 4f91febe7ba34b5ba5ae14368508cc09e5339c4b
iuc
parents:
diff changeset
82 </tool>