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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu commit 4290547cefb0459595f28fbba063f2cf58b35086
author iuc
date Tue, 13 Aug 2024 13:44:35 +0000
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-1:000000000000 0:d4cc7bbf4a14
1 <tool id="pacu_map" name="PACU - mapping" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Map ONT / Illumina reads to a reference genome for PACU</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro='xrefs'/>
7 <expand macro="requirements" />
8 <expand macro="version_command"/>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 PACU_map
12
13 ## FASTA input
14 --ref-fasta '$ref_fasta'
15 --ref-fasta-name '$ref_fasta.element_identifier'
16
17 ## FASTQ input
18 --read-type $fastq_tech.read_type
19 #if str($fastq_tech.read_type) == 'illumina':
20 --fastq-illumina $fastq_tech.fastq_illumina_1 $fastq_tech.fastq_illumina_2
21 --fastq-illumina-names '$fastq_tech.fastq_illumina_1.element_identifier' '$fastq_tech.fastq_illumina_2.element_identifier'
22 #elif str($fastq_tech.read_type) == 'ont':
23 --fastq-ont $fastq_tech.fastq_ont
24 --fastq-ont-name '$fastq_tech.fastq_ont.element_identifier'
25 #end if
26
27 ## Output
28 --output '$bam'
29
30 ## Other options
31 $trim
32 --dir-working \$PWD
33 --threads \${GALAXY_SLOTS}
34 ]]>
35 </command>
36 <inputs>
37 <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
38 <conditional name="fastq_tech">
39 <param argument="--read-type" type="select" label="FASTQ type">
40 <option value="illumina">Illumina paired-end reads</option>
41 <option value="ont">ONT single-end reads</option>
42 </param>
43 <when value="illumina">
44 <param name="fastq_illumina_1" type="data" format="fastq,fastqsanger.gz" label="Forward reads"/>
45 <param name="fastq_illumina_2" type="data" format="fastq,fastqsanger.gz" label="Reverse reads"/>
46 </when>
47 <when value="ont">
48 <param name="fastq_ont" type="data" format="fastq,fastqsanger.gz" label="ONT reads"/>
49 </when>
50 </conditional>
51 <param argument="--trim" type="boolean" label="Trim reads" checked="true" truevalue="--trim" falsevalue=""/>
52 </inputs>
53 <outputs>
54 <data name="bam" format="bam" label="Mapping on ${on_string}"/>
55 </outputs>
56 <tests>
57 <test>
58 <!-- The line differences correspond to the three commands in the SAM header -->
59 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
60 <conditional name="fastq_tech">
61 <param name="read_type" value="ont"/>
62 <param name="fastq_ont" value="TIAC1151-ont.gz"/>
63 </conditional>
64 <param name="trim" value="false" />
65 <output name="bam" ftype="bam" file="mapped_reads-ont.bam" lines_diff="6"/>
66 </test>
67 <test>
68 <!-- The line differences correspond to the three commands in the SAM header -->
69 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
70 <conditional name="fastq_tech">
71 <param name="read_type" value="illumina"/>
72 <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
73 <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
74 </conditional>
75 <param name="trim" value="false" />
76 <output name="bam" ftype="bam" file="mapped_reads-ilmn.bam" lines_diff="6"/>
77 </test>
78 <test>
79 <!-- The line differences correspond to the three commands in the SAM header -->
80 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
81 <conditional name="fastq_tech">
82 <param name="read_type" value="ont"/>
83 <param name="fastq_ont" value="TIAC1151-ont.gz"/>
84 </conditional>
85 <param name="trim" value="true" />
86 <output name="bam" ftype="bam" file="mapped_reads_trimmed-ont.bam" lines_diff="6"/>
87 </test>
88 <test>
89 <!-- The line differences correspond to the three commands in the SAM header -->
90 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
91 <conditional name="fastq_tech">
92 <param name="read_type" value="illumina"/>
93 <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
94 <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
95 </conditional>
96 <param name="trim" value="true" />
97 <output name="bam" ftype="bam" file="mapped_reads_trimmed-ilmn.bam" lines_diff="6"/>
98 </test>
99 </tests>
100 <help>
101 This script maps Illumina or ONT reads to an input reference genome in FASTA format.
102 It also writes a custom tag to the BAM file to propagate the sample name to PACU within Galaxy.
103 The sample name is derived from the name of the input FASTQ files.
104 </help>
105 <expand macro="citations"/>
106 </tool>