Mercurial > repos > iuc > halfdeep
changeset 0:607d5e33c4c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep commit 63179f3d35e5dec09cdd01c07c6a4e8af3da777d
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 16:57:06 +0000 |
| parents | |
| children | a53e299fe1cb |
| files | halfdeep.xml macros.xml test-data/halfdeep.bed test-data/mapped_reads.bam test-data/reads.fasta.gz test-data/ref.fasta.gz |
| diffstat | 5 files changed, 113 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/halfdeep.xml Thu Dec 05 16:57:06 2024 +0000 @@ -0,0 +1,90 @@ +<tool id="halfdeep" name="HalfDeep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>identifies genomic regions with half-depth coverage based on sequencing read mappings.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ## + ## Set up the directory structure expected by bam_depth.sh and halfdeep.sh + ## See: https://github.com/makovalab-psu/HalfDeep?tab=readme-ov-file#expected-directory-layout + ## + mkdir -p reads halfdeep/ref/mapped_reads && + ## + ## reference + ## + ln -s '$ref' 'ref.$ref.ext' && + #if not $mapped_reads + minimap2 -x map-pb -d ref.idx 'ref.$ref.ext' && + #else + touch ref.idx && + #end if + ## + ## reads + ## + #import re + #set $reads_base = re.sub('[^\w\-\s]', '_', str($reads.element_identifier)) + ln -s '$reads' 'reads/${reads_base}.$reads.ext' && + echo 'reads/${reads_base}.$reads.ext' >> input.fofn && + ## + ## mapped reads + ## + #if $mapped_reads + ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' && + ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' && + ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' && + #end if + ## + ## run bam_depth.sh + ## + bam_depth.sh 'ref.$ref.ext' 1 && + ## + ## run halfdeep.sh + ## + halfdeep.sh 'ref.$ref.ext' + ]]></command> + <inputs> + <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/> + <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/> + <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."/> + </inputs> + <outputs> + <data name="halfdeep_dat" format="bed" from_work_dir="halfdeep/ref/halfdeep.dat" label="HalfDeep on ${on_string}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/> + <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/> + <param name="mapped_reads" value="mapped_reads.bam" ftype="bam"/> + <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/> + </test> + <test expect_num_outputs="1"> + <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/> + <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/> + <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/> + </test> + </tests> + <help><![CDATA[ + +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. + +Given the following inputs: + +1. A genome assembly in FASTA format. +2. Reads in FASTQ format. +3. Mapped reads in BAM format (optional) + +HalfDeep automates the following tasks: + +1. Mapping reads and merging individual mapping files. +2. Calculating per-base read depth. +3. Smoothing read coverage using a defined window with genodsp. +4. Determining the percentile of read coverage. +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 + +HalfDeep produces the following output: + +1. HalfDeep: BED file containing regions of the genome assembly that are "covered at half depth" + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Dec 05 16:57:06 2024 +0000 @@ -0,0 +1,23 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">halfdeep</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.05</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{github_halfdeep, + author = {Makova Lab PSU}, + year = "2019", + title = {HalfDeep}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/makovalab-psu/HalfDeep} + </citation> + </citations> + </xml> +</macros>