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planemo upload commit 1f45ac19d30ec5c5bf7d44a0b09990369a139668
author jpayne
date Mon, 08 Dec 2025 20:22:33 +0000
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1 <tool id="reads_subsampler" name="GalaxyTrakr Subsampler" version="1.0.0" python_template_version="3.5">
2 <description>to reduce excess genomic coverage to specified depth</description>
3 <requirements>
4 <requirement type="package" version="3.7">python</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #if $reads.reads_select == 'collection'
8 python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed'
9 #elif $reads.reads_select == 'single'
10 python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
11 #else
12 python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed'
13 #end if
14 ]]></command>
15 <inputs>
16 <conditional name="reads">
17 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
18 <option value="collection">Paired collection from your history</option>
19 <option value="history">Two FASTQ datasets from your history representing paired reads, forward and reverse</option>
20 <option value="single">One FASTQ dataset representing single-end sequencing</option>
21 </param>
22 <when value="collection">
23 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
24 </when>
25 <when value="history">
26 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
27 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
28 </when>
29 <when value="single">
30 <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
31 </when>
32 </conditional>
33 <param name="coverage" type="integer" label="Maximum Coverage" value="200" />
34 <param name="genome_size" type="select" label="Assumed Genome Size">
35 <option value="5000000">Salmonella, E. Coli, Vibrio p. (5000000)</option>
36 <option value="4000000">Vibrio cholerae (4000000)</option>
37 <option value="2700000">Listeria (2700000)</option>
38 <option value="1600000">Campylobacter (1600000)</option>
39 <option value="29900">SARS-CoV-2 (29900)</option>
40 </param>
41 <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/>
42 </inputs>
43 <outputs>
44 <data name="forward_out" label="${reads.forward.name}.downsampled" format_source="forward">
45 <filter>reads['reads_select'] == "history" or reads['reads_select'] == "single"</filter>
46 </data>
47 <data name="reverse_out" label="${reads.reverse.name}.downsampled" format_source="reverse">
48 <filter>reads['reads_select'] == "history"</filter>
49 </data>
50 <collection name="downsampled" type="paired" label="${reads.coll.name}" structured_like="reads|coll" format_source="reads|coll">
51 <filter>reads['reads_select'] == "collection"</filter>
52 <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" />
53 <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" />
54 </collection>
55 </outputs>
56 <tests>
57 <test>
58 <conditional name="reads">
59 <param name="reads_select" value="single" />
60 <param name="forward" value="forward.fastq" />
61 </conditional>
62 <param name="coverage" value="20" />
63 <param name="genome_size" value="29900" />
64 <output name="forward_out" value="forward_out.fastq" />
65 </test>
66 <test>
67 <conditional name="reads">
68 <param name="reads_select" value="collection" />
69 <param name="coll">
70 <collection type="paired">
71 <element name="forward" value="forward.fastq" ftype="fastqsanger" />
72 <element name="reverse" value="reverse.fastq" ftype="fastqsanger" />
73 </collection>
74 </param>
75 </conditional>
76 <param name="coverage" value="20" />
77 <param name="genome_size" value="29900" />
78 <output_collection name="downsampled" type="paired">
79 <element name="forward" file="forward_out.fastq" />
80 <element name="reverse" file="reverse_out.fastq" />
81 </output_collection>
82 </test>
83 <test>
84 <conditional name="reads">
85 <param name="reads_select" value="history" />
86 <param name="forward" value="forward.fastq" />
87 <param name="reverse" value="reverse.fastq" />
88 </conditional>
89 <param name="coverage" value="20" />
90 <param name="genome_size" value="29900" />
91 <output name="forward_out" value="forward_out.fastq" />
92 <output name="reverse_out" value="reverse_out.fastq" />
93 </test>
94 <test>
95 <conditional name="reads">
96 <param name="reads_select" value="history" />
97 <param name="forward" value="forward.fastq.gz" />
98 <param name="reverse" value="reverse.fastq.gz" />
99 </conditional>
100 <param name="coverage" value="20" />
101 <param name="genome_size" value="29900" />
102 <output name="forward_out" value="forward_out.fastq.gz" decompress="true" />
103 <output name="reverse_out" value="reverse_out.fastq.gz" decompress="true" />
104 </test>
105 <test>
106 <conditional name="reads">
107 <param name="reads_select" value="history" />
108 <param name="forward" value="forward.fastq.bz2" />
109 <param name="reverse" value="reverse.fastq.bz2" />
110 </conditional>
111 <param name="coverage" value="20" />
112 <param name="genome_size" value="29900" />
113 <output name="forward_out" value="forward_out.fastq.bz2" decompress="true" />
114 <output name="reverse_out" value="reverse_out.fastq.bz2" decompress="true" />
115 </test>
116 </tests>
117 <help><![CDATA[
118 Randomly subsample single or paired-end FASTQ reads to target a certain genomic coverage depth.
119 ]]></help>
120 <citations />
121 </tool>