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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 42ce963fae778982b4aab4ef3b1e88480dea5053
author galaxy-australia
date Mon, 11 Nov 2024 03:05:14 +0000
parents 1957f881bdf4
children
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0:1957f881bdf4 1:7ff7680fa713
1 <tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1"> 1 <tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1">
2 <description>for Oxford Nanopore (ONT) DNA reads</description> 2 <description>for Oxford Nanopore (ONT) DNA reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
12 && 12 &&
13 13
14 dorado trim 14 dorado trim
15 --verbose 15 --verbose
16 --threads "\${GALAXY_SLOTS}" 16 --threads "\${GALAXY_SLOTS}"
17 #if $no_trim_primers 17 #if $trim_primers.no_trim_primers == 'dont_trim'
18 --no-trim-primers 18 --no-trim-primers
19 #end if 19 #else if $trim_primers.primer_sequences
20 #if $primer_sequences 20 --primer-sequences '${trim_primers.primer_sequences}'
21 --primer-sequences '$primer_sequences'
22 #end if 21 #end if
23 reads 22 reads
24 > trimmed.bam 23 > trimmed.bam
25 24
26 && 25 &&
31 30
32 31
33 ]]></command> 32 ]]></command>
34 <inputs> 33 <inputs>
35 <param name="reads" type="data" format="bam,fastqsanger,unsorted.bam" label="Existing, basecalled DNA dataset" help="Note: this tool does not support trimming adaptors from RNA reads. These need to be removed during basecalling."/> 34 <param name="reads" type="data" format="bam,fastqsanger,unsorted.bam" label="Existing, basecalled DNA dataset" help="Note: this tool does not support trimming adaptors from RNA reads. These need to be removed during basecalling."/>
36 <param argument="--no-trim-primers" type="boolean" label="Don't trim primers" help="This option can be used to prevent the trimming of primer sequences. In this case only adapter sequences will be trimmed."/> 35 <conditional name="trim_primers">
37 <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/> 36 <param argument="--no-trim-primers" type="select" label="Enable primer trimming" help="Selecting 'No' prevents the trimming of primer sequences. In this case only adapter sequences will be trimmed.">
37 <option value="trim" selected="true">Yes</option>
38 <option value="dont_trim">No</option>
39 </param>
40 <when value="trim">
41 <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/>
42 </when>
43 <when value="dont_trim"/>
44 </conditional>
38 </inputs> 45 </inputs>
39 <outputs> 46 <outputs>
40 <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} trimmed by the ${tool.name} tool" from_work_dir="trimmed.bam"/> 47 <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} trimmed by the ${tool.name} tool" from_work_dir="trimmed.bam"/>
41 <data format="tsv" name="out_tsv" label="${tool.name} sequencing summary for ${on_string}" from_work_dir="summary.tsv"/> 48 <data format="tsv" name="out_tsv" label="${tool.name} sequencing summary for ${on_string}" from_work_dir="summary.tsv"/>
42 </outputs> 49 </outputs>
43 <tests> 50 <tests>
44 <test expect_num_outputs="2"> 51 <test expect_num_outputs="2">
45 <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> 52 <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/>
46 <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test1.bam"/> 53 <output name="out_bam" ftype="unsorted.bam">
47 <output name="out_tsv" ftype="tsv" file="dorado_trimming_test1.tsv"/> 54 <assert_contents>
55 <has_size size="60725" delta="6000"/>
56 </assert_contents>
57 </output>
58 <output name="out_tsv" ftype="tsv">
59 <assert_contents>
60 <has_text text="002f231b-5d37-437f-a027-a2e8b872e73b"/>
61 </assert_contents>
62 </output>
48 </test> 63 </test>
49 <test expect_num_outputs="2"> 64 <test expect_num_outputs="2">
50 <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/> 65 <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/>
51 <param name="no_trim_primers" value="True"/> 66 <param name="no_trim_primers" value="dont_trim"/>
52 <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test2.bam"/> 67 <output name="out_bam" ftype="unsorted.bam">
53 <output name="out_tsv" ftype="tsv" file="dorado_trimming_test2.tsv"/> 68 <assert_contents>
69 <has_size size="60628" delta="6000"/>
70 </assert_contents>
71 </output>
72 <output name="out_tsv" ftype="tsv">
73 <assert_contents>
74 <has_text text="00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf"/>
75 </assert_contents>
76 </output>
54 </test> 77 </test>
55 <test expect_num_outputs="2"> 78 <test expect_num_outputs="2">
56 <param name="reads" value="lsk109_single_read.fastqsanger.gz" ftype="fastqsanger.gz"/> 79 <param name="reads" value="lsk109_single_read.fastqsanger.gz" ftype="fastqsanger.gz"/>
57 <param name="primer_sequences" value="custom_primers.fasta.gz" ftype="fasta.gz"/> 80 <param name="primer_sequences" value="custom_primers.fasta.gz" ftype="fasta.gz"/>
58 <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test3.bam"/> 81 <output name="out_bam" ftype="unsorted.bam">
59 <output name="out_tsv" ftype="tsv" file="dorado_trimming_test3.tsv"/> 82 <assert_contents>
83 <has_size size="798" delta="100"/>
84 </assert_contents>
85 </output>
86 <output name="out_tsv" ftype="tsv">
87 <assert_contents>
88 <has_text text="2f707b6e-0060-4f33-9c92-a1230d26cb21"/>
89 </assert_contents>
90 </output>
60 </test> 91 </test>
61 </tests> 92 </tests>
62 <help><![CDATA[ 93 <help><![CDATA[
63 Detect and remove any adapter and/or primer sequences from the beginning 94 Detect and remove any adapter and/or primer sequences from the beginning
64 and end of DNA reads using Oxford Nanopore’s open source 95 and end of DNA reads using Oxford Nanopore’s open source
73 Note that if you intend to demultiplex the reads later, trimming 104 Note that if you intend to demultiplex the reads later, trimming
74 adapters and primers may result in some portions of the flanking regions 105 adapters and primers may result in some portions of the flanking regions
75 of the barcodes being removed, which could interfere with correct 106 of the barcodes being removed, which could interfere with correct
76 demultiplexing. 107 demultiplexing.
77 108
78 The **Don't trim primers** option can be used to prevent the trimming of 109 The **Enable primer trimming** option can be set to 'No' to prevent the
79 primer sequences. In this case only adapter sequences will be trimmed. 110 trimming of primer sequences. If you select 'No', only adapter sequences will
111 be trimmed.
80 112
81 The output of will always be unaligned records, regardless of whether 113 The output of will always be unaligned records, regardless of whether
82 the input is aligned/sorted or not. 114 the input is aligned/sorted or not.
83 115
84 Custom primer trimming 116 Custom primer trimming