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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 13:44:47 +0000
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1 <tool id="pacu_snp" name="PACU" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data</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_galaxy
12
13 ## Input files
14 --ref-fasta '$input.ref_fasta'
15 --ref-fasta-name '$input.ref_fasta.element_identifier'
16
17 #for $bam in $input.bam_ilmn:
18 #if $bam:
19 --bam-ilmn $bam '$bam.element_identifier'
20 #end if
21 #end for
22
23 #for $bam in $input.bam_ont:
24 #if $bam:
25 --bam-ont $bam '$bam.element_identifier'
26 #end if
27 #end for
28
29 ## Excluded regions
30 #if $input.ref_bed:
31 --ref-bed $input.ref_bed
32 #end if
33
34 ## Tree building method
35 #if $params.tree_method == 'mega':
36 --use-mega
37 #end if
38
39 ## Other parameters
40 --min-global-depth $params.min_global_depth
41 $params.skip_gubbins
42
43 ## Output files
44 --output-html '$html'
45 --output '$html.files_path'
46
47 ## Variant filters
48 --min-snp-af $filtering.min_snp_af
49 --min-snp-qual $filtering.min_snp_qual
50 --min-snp-depth $filtering.min_snp_depth
51 --min-snp-dist $filtering.min_snp_dist
52
53 ## Other options
54 --threads \${GALAXY_SLOTS}
55 ]]>
56 </command>
57 <inputs>
58 <!-- Input files -->
59 <section name="input" title="Input files" expanded="true">
60 <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
61 <param argument="--bam-ilmn" type="data" format="bam" multiple="true" optional="true"
62 label="BAM files (Illumina)"
63 help="Make sure the reads are mapped to the reference selected above."/>
64 <param argument="--bam-ont" type="data" format="bam" multiple="true" optional="true" label="BAM files (ONT)"
65 help="Make sure the reads are mapped to the reference selected above."/>
66 <param argument="--ref-bed" type="data" format="bed" optional="true" label="Excluded regions BED file" help="BED file with (pro)phage or other regions in the reference genome to be omitted from the SNP analysis."/>
67 </section>
68
69 <!-- Parameters -->
70 <section name="params" title="Parameters" expanded="False">
71 <param name="tree_method" type="select" label="Tree building method"
72 help="MEGA is not part of the Conda installation and may be unavailable.">
73 <option value="iqtree" selected="true">IQ-TREE</option>
74 <option value="mega">MEGA X</option>
75 </param>
76 <param argument="--skip-gubbins" type="boolean" label="Skip Gubbins" checked="false"
77 truevalue="--skip-gubbins" falsevalue=""
78 help="Skips recombination detection using Gubbins, this option can be used to work with fragmented reference genomes."/>
79 <param argument="--min-global-depth" type="integer" label="Min. global depth" value="5" min="0" max="100"
80 help="Minimum depth across all samples for a position to be included in the SNP analysis."/>
81 </section>
82
83 <!-- Variant filtering -->
84 <section name="filtering" title="Variant filters" expanded="false">
85 <param argument="--min-snp-af" type="float" value="0.66" min="0.0" max="1.0" label="Min. allele frequency"/>
86 <param argument="--min-snp-depth" type="integer" value="5" min="0" label="Min. depth"/>
87 <param argument="--min-snp-qual" type="integer" value="50" min="0" max="255" label="Min. SNP quality"/>
88 <param argument="--min-snp-dist" type="integer" value="10" min="0" max="100"
89 label="Min. distance between SNPs"/>
90 </section>
91 </inputs>
92
93 <outputs>
94 <data name="html" format="html" label="PACU (${input.ref_fasta.element_identifier})"/>
95 </outputs>
96 <tests>
97 <test>
98 <section name="input">
99 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
100 <param name="bam_ilmn" value="TIAC1151.bam,TIAC1153.bam,TIAC1660.bam"/>
101 <param name="bam_ont" value="TIAC1638-R9-ds.bam,TIAC1151-R10-ds.bam"/>
102 </section>
103 <section name="params">
104 <param name="tree_method" value="iqtree"/>
105 </section>
106 <output name="html" ftype="html">
107 <assert_contents>
108 <has_text text="PACU report"/>
109 </assert_contents>
110 </output>
111 </test>
112 <test>
113 <section name="input">
114 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
115 <param name="ref_bed" value="NC_002695.2-sample.bed"/>
116 <param name="bam_ilmn" value="TIAC1151.bam,TIAC1153.bam,TIAC1660.bam"/>
117 <param name="bam_ont" value="TIAC1638-R9-ds.bam,TIAC1151-R10-ds.bam"/>
118 </section>
119 <section name="params">
120 <param name="tree_method" value="iqtree"/>
121 </section>
122 <output name="html" ftype="html">
123 <assert_contents>
124 <has_text text="PACU report"/>
125 </assert_contents>
126 </output>
127 </test>
128 </tests>
129 <help>
130 **Warning:** At least four input BAM files are required for bootstrapping (these can be a mix of Illumina / ONT
131 datasets).
132
133 **Note:** You can use the *'PACU - mapping'* tool in Galaxy to map Illumina or ONT reads to the reference
134 genome.
135 </help>
136 <expand macro="citations"/>
137 </tool>