Mercurial > repos > iuc > halfdeep

comparison halfdeep.xml @ 0:6b6c3cf23fe8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep commit 63179f3d35e5dec09cdd01c07c6a4e8af3da777d
author iuc
date Thu, 05 Dec 2024 16:56:55 +0000
parents
children 405c082a9a20
comparison
equal deleted inserted replaced
-1:000000000000 0:6b6c3cf23fe8
1 <tool id="halfdeep" name="HalfDeep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>identifies genomic regions with half-depth coverage based on sequencing read mappings.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 ##
9 ## Set up the directory structure expected by bam_depth.sh and halfdeep.sh
10 ## See: https://github.com/makovalab-psu/HalfDeep?tab=readme-ov-file#expected-directory-layout
11 ##
12 mkdir -p reads halfdeep/ref/mapped_reads &&
13 ##
14 ## reference
15 ##
16 ln -s '$ref' 'ref.$ref.ext' &&
17 #if not $mapped_reads
18 minimap2 -x map-pb -d ref.idx 'ref.$ref.ext' &&
19 #else
20 touch ref.idx &&
21 #end if
22 ##
23 ## reads
24 ##
25 #import re
26 #set $reads_base = re.sub('[^\w\-\s]', '_', str($reads.element_identifier))
27 ln -s '$reads' 'reads/${reads_base}.$reads.ext' &&
28 echo 'reads/${reads_base}.$reads.ext' >> input.fofn &&
29 ##
30 ## mapped reads
31 ##
32 #if $mapped_reads
33 ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' &&
34 ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' &&
35 ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' &&
36 #end if
37 ##
38 ## run bam_depth.sh
39 ##
40 bam_depth.sh 'ref.$ref.ext' 1 &&
41 ##
42 ## run halfdeep.sh
43 ##
44 halfdeep.sh 'ref.$ref.ext'
45 ]]></command>
46 <inputs>
47 <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/>
48 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
49 <param name="mapped_reads" type="data" format="bam" value="" optional="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
50 </inputs>
51 <outputs>
52 <data name="halfdeep_dat" format="bed" from_work_dir="halfdeep/ref/halfdeep.dat" label="HalfDeep on ${on_string}"/>
53 </outputs>
54 <tests>
55 <test expect_num_outputs="1">
56 <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
57 <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
58 <param name="mapped_reads" value="mapped_reads.bam" ftype="bam"/>
59 <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
60 </test>
61 <test expect_num_outputs="1">
62 <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
63 <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
64 <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68
69 HalfDeep identifies genomic regions with half-depth coverage based on sequencing read mappings. These regions may reveal insights into heterogametic sex chromosomes, haplotype-specific variation, or potential assembly errors such as heterotypic duplications.
70
71 Given the following inputs:
72
73 1. A genome assembly in FASTA format.
74 2. Reads in FASTQ format.
75 3. Mapped reads in BAM format (optional)
76
77 HalfDeep automates the following tasks:
78
79 1. Mapping reads and merging individual mapping files.
80 2. Calculating per-base read depth.
81 3. Smoothing read coverage using a defined window with genodsp.
82 4. Determining the percentile of read coverage.
83 5. Identifying genomic regions with half-depth coverage based on a specified percentile threshold (e.g., 40–60%) and exporting them in BED file format
84
85 HalfDeep produces the following output:
86
87 1. HalfDeep: BED file containing regions of the genome assembly that are "covered at half depth"
88 ]]></help>
89 <expand macro="citations"/>
90 </tool>