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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fur commit 24966e011387cb768be93e3aaf0de97b5fc3e5ef
author iuc
date Mon, 16 Feb 2026 12:14:40 +0000
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1 <tool id="fur" name="Fur" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>find unique genomic regions from target and neighbor genomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">fur</xref>
8 </xrefs>
9 <expand macro="requirements"/>
10 <version_command>fur -v</version_command>
11 <command><![CDATA[
12 mkdir -p 'work/targets' 'work/neighbors' 'out' &&
13 #for $target_index, $target in enumerate($t):
14 ln -s '$target' 'work/targets/target_${target_index}.fa' &&
15 #end for
16
17 #for $neighbor_index, $neighbor in enumerate($n):
18 ln -s '$neighbor' 'work/neighbors/neighbor_${neighbor_index}.fa' &&
19 #end for
20
21 makeFurDb
22 -t 'work/targets'
23 -n 'work/neighbors'
24 -d 'work/fur.db'
25 -T "\${GALAXY_SLOTS:-1}"
26 2> 'out/summary.txt' &&
27
28 fur -d 'work/fur.db'
29 -w '$analysis.window_length'
30 -q '$analysis.quantile'
31 -e '$analysis.evalue'
32 -n '$analysis.min_region_length'
33 -t "\${GALAXY_SLOTS:-1}"
34 $analysis.exact_matches_only
35 $analysis.megablast_only
36 $analysis.mask_neighbors
37 > 'out/unique_regions.fasta' 2>> 'out/summary.txt'
38 ]]></command>
39 <inputs>
40 <param argument="-t" type="data" multiple="true" format="fasta" label="Target genome FASTA files" help="One or more target genomes used to discover shared unique regions."/>
41 <param argument="-n" type="data" multiple="true" format="fasta" label="Neighbor genome FASTA files" help="One or more closely related neighbor genomes used for subtraction."/>
42 <section name="analysis" title="Analysis options" expanded="true">
43 <param argument="-w" name="window_length" type="integer" min="1" value="80" label="Sliding window length" help="Window size used in the first subtraction step."/>
44 <param argument="-q" name="quantile" type="float" min="0" max="1" value="0.1" label="Quantile of match length distribution" help="Lower values are more stringent in the first subtraction step."/>
45 <param argument="-e" name="evalue" type="float" min="0" value="1e-5" label="BLAST E-value" help="E-value threshold used in the final subtraction step."/>
46 <param argument="-n" name="min_region_length" type="integer" min="1" value="100" label="Minimum region length" help="Only regions with at least this many nucleotides are reported."/>
47 <param argument="-x" name="exact_matches_only" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Keep only exact matches during target intersection"/>
48 <param argument="-m" name="megablast_only" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Use only megablast for the final subtraction"/>
49 <param argument="-M" name="mask_neighbors" type="boolean" truevalue="-M" falsevalue="" checked="false" label="Enable masked BLAST database search" help="Recommended for mammalian genomes when masking information is available."/>
50 </section>
51 </inputs>
52 <outputs>
53 <data name="unique_regions" format="fasta" from_work_dir="out/unique_regions.fasta" label="${tool.name} on ${on_string}: unique regions"/>
54 <data name="summary" format="txt" from_work_dir="out/summary.txt" label="${tool.name} on ${on_string}: run summary"/>
55 </outputs>
56 <tests>
57 <test expect_num_outputs="2">
58 <param name="t" value="target_0.fa,target_1.fa" ftype="fasta"/>
59 <param name="n" value="neighbor_0.fa" ftype="fasta"/>
60 <output name="unique_regions" file="exp_unique_regions_default.fasta"/>
61 <output name="summary">
62 <assert_contents>
63 <has_text text="Subtraction_2"/>
64 </assert_contents>
65 </output>
66 </test>
67 <test expect_num_outputs="2">
68 <param name="t" value="target_0.fa,target_1.fa" ftype="fasta"/>
69 <param name="n" value="neighbor_0.fa" ftype="fasta"/>
70 <section name="analysis">
71 <param name="min_region_length" value="150"/>
72 </section>
73 <output name="unique_regions" file="exp_unique_regions_n150.fasta"/>
74 <output name="summary">
75 <assert_contents>
76 <has_text text="Intersection 0"/>
77 </assert_contents>
78 </output>
79 </test>
80 </tests>
81 <help format="markdown"><![CDATA[
82 `Fur` discovers genomic regions that are shared by target genomes but absent from neighbor genomes.
83
84 This wrapper runs the full Fur workflow in one step:
85
86 1. Build a temporary Fur database with `makeFurDb` from target and neighbor FASTA collections.
87 2. Run `fur` on that database to report unique regions.
88
89 ### Inputs
90
91 - **Target genome FASTA files**: one or more genomes that define the group of interest.
92 - **Neighbor genome FASTA files**: one or more related genomes that should not contain the marker.
93
94 ### Outputs
95
96 - **Unique regions**: FASTA file with candidate marker regions.
97 - **Run summary**: textual report from `makeFurDb` and `fur`, including per-step counts.
98
99 ### Notes
100 - The temporary Fur database is created inside the job working directory and is not retained as an output.
101 ]]></help>
102 <expand macro="citations"/>
103 </tool>