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1 <tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0">
2 <description>Extract splice junctions from a RNA-Seq BAM file</description>
3 <requirements>
4 <requirement type="package" version="0.3.0">regtools</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 ## regtools expects an indexed BAM file
11 ## Use symlinks to link the BAM file and its index to the working directory
12 ## See: https://biostar.usegalaxy.org/p/10128/
13
14 ln -sf '${input1}' infile.bam &&
15 ln -sf '${input1.metadata.bam_index}' infile.bam.bai &&
16
17 regtools junctions extract
18 -i $min_intron_length
19 -I $max_intron_length
20 -o $output1
21 #if str($advanced_options.advanced_options_selector) == "on":
22 -a $advanced_options.min_anchor_length
23
24 #if str($advanced_options.region):
25 -r "$advanced_options.region"
26 #end if
27 #end if
28 infile.bam
29 ]]></command>
30 <inputs>
31 <param name="input1" type="data" format="bam" />
32
33 <param name="min_intron_length" type="integer" label="Minimum intron length" value="20" min="1">
34 <help>Only considers spliced RNA-Seq reads with this minimum intron length (-i)</help>
35 </param>
36 <param name="max_intron_length" type="integer" label="Maximum intron length" value="500000" min="1">
37 <help>Only considers spliced RNA-Seq reads with this maximum intron length (-I)</help>
38 </param>
39
40 <conditional name="advanced_options">
41 <param name="advanced_options_selector" type="select" label="Advanced options">
42 <option value="off" selected="true">Hide advanced options</option>
43 <option value="on">Display advanced options</option>
44 </param>
45 <when value="on">
46 <param name="min_anchor_length" type="integer" label="Minimum anchor length" value="8" min="1">
47 <help>Only report splice junctions with this minimum anchor length on both sides of the junction (-a)</help>
48 </param>
49 <param name="region" type="text" optional="true" label="Only extract junctions in this region" value="">
50 <help>Only report splice junctions within this region (format = chrom:start-end) (-r)</help>
51 <validator type="regex"
52 message="Region should be in the following format: chrom:start-end">^([^:]+):(\d+)-(\d+)$</validator>
53 </param>
54 </when>
55
56 <when value="off" />
57 </conditional>
58 </inputs>
59 <outputs>
60 <data name="output1" format="bed" />
61 </outputs>
62 <tests>
63 <test>
64 <!-- Test with default parameters -->
65 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
66 <output name="output1" file="Dbia3_adult_males_junctions_i20_I500000.bed" />
67 </test>
68 <test>
69 <!-- Test with custom intron length thresholds -->
70 <param name="min_intron_length" value="50" />
71 <param name="max_intron_length" value="50000" />
72 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
73 <output name="output1" file="Dbia3_adult_males_junctions_i50_I50000.bed" />
74 </test>
75 <test>
76 <!-- Test with advanced option and custom anchor size -->
77 <param name="advanced_options_selector" value="on" />
78 <param name="min_anchor_length" value="10" />
79 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
80 <output name="output1"
81 file="Dbia3_adult_males_junctions_i20_I500000_a10.bed" />
82 </test>
83 <test>
84 <!-- Test with advanced option and selected region -->
85 <param name="advanced_options_selector" value="on" />
86 <param name="region" value="contig2:10000-30000" />
87 <param name="input1" value="Dbia3_adult_males_shallow.bam" />
88 <output name="output1"
89 file="Dbia3_adult_males_junctions_i20_I500000_rcontig2_10-30kb.bed" />
90 </test>
91 </tests>
92 <help><![CDATA[
93 **What it does**
94
95 The `regtools junctions extract <https://regtools.readthedocs.io/en/latest/commands/junctions-extract/>`_
96 tool creates a list of exon-exon junctions from spliced RNA-Seq reads within a BAM
97 alignment file. The format of the output BED file is similar to the ``junctions.bed``
98 file produced by TopHat2.
99
100 The extent of each BED feature corresponds to the maximum overhang of each splice
101 junction. The score of each BED feature corresponds to the number of spliced RNA-Seq
102 reads that support each junction.
103
104 --------
105
106 .. class:: warningmark
107
108 By default, the minimum intron size is **20 bp** and the maximum intron size is
109 **500,000 bp** so that they conform to the default intron size settings for
110 `HISAT2 <https://ccb.jhu.edu/software/hisat2/manual.shtml#options>`_. The minimum
111 intron size for the command-line version of ``regtools junctions extract`` is 70 bp.
112
113 ]]></help>
114 <citations>
115 <citation type="bibtex">
116 @misc{githubregtools,
117 author = {Griffith Lab},
118 year = {2016},
119 title = {regtools},
120 publisher = {GitHub},
121 journal = {GitHub repository},
122 url = {https://github.com/griffithlab/regtools},
123 }</citation>
124 </citations>
125 </tool>