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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 73721d980c1f422dc880d80f61e44d270992e537
| author | artbio |
|---|---|
| date | Sat, 20 Apr 2024 11:56:53 +0000 |
| parents | |
| children | 6d59fbca2db4 |
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<tool id="repenrich2" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Repeat Element Profiling</description> <macros> <import>macros.xml</import> </macros> <expand macro="repenrich_requirements"/> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ #import re ## uncompress fastq.gz or fastqsanger.gz is not required with bowtie2 #if $seq_method.seq_method_list == "single-read": ln -f -s '$seq_method.input_fastq' 'input.fastq' && #elif $seq_method.seq_method_list == 'paired_collection': ln -f -s '$seq_method.input_fastq.forward' 'input.fastq' && ln -f -s '$seq_method.input_fastq.reverse' 'input_2.fastq' && #else: ln -f -s '$seq_method.input_fastq' 'input.fastq' && ln -f -s '$seq_method.input2_fastq' 'input_2.fastq' && #end if #if $refGenomeSource.genomeSource == "history": bowtie2-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource.genome genome 1>/dev/null && ln -s -f '$refGenomeSource.genome' 'genome.fa' && #set index_path = 'genome' #else: #set index_path = $refGenomeSource.index.fields.path bowtie-inspect $index_path > genome.fa && #end if python $__tool_directory__/RepEnrich2_setup.py --annotation_file '$repeatmasker' --genomefasta 'genome.fa' --cpus "\${GALAXY_SLOTS:-4}" && #if $seq_method.seq_method_list == "single-read": bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam && samtools view -@ "\${GALAXY_SLOTS:-4}" -h -F 4 -b aligned.bam \ | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ | bedtools bamtofastq -i /dev/stdin -fq multimap.fastq && #else: bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam && samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam \ | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ | samtools sort -@ "\${GALAXY_SLOTS:-4}" -n - - | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq && #end if samtools index unique.bam && python $__tool_directory__/RepEnrich2.py --annotation_file $repeatmasker --alignment_bam unique.bam --cpus "\${GALAXY_SLOTS:-4}" #if $seq_method.seq_method_list == "single-read": --fastqfile multimap.fastq #else: --fastqfile multimap_1.fastq --fastqfile2 multimap_2.fastq #end if ]]></command> <!-- basic error handling --> <inputs> <conditional name="seq_method"> <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> <option selected="True" value="single-read">Single-read sequencing</option> <option value="paired-end">Paired-end sequencing</option> <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single-read"> <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> </when> <when value="paired-end"> <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> </when> <when value="paired_collection"> <param name="input_fastq" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype "fastqsanger" or "fasta"" /> </when> </conditional> <conditional name="refGenomeSource"> <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select"> <option value="indexed">Use a built-in index</option> <option value="history">Use one from the history</option> </param> <when value="indexed"> <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="genome" type="select"> <options from_data_table="bowtie2_indexes" /> </param> </when> <when value="history"> <param format="fasta" label="Select a fasta file, to serve as index reference" name="genome" type="data" /> </when> </conditional> <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> </inputs> <outputs> <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" /> <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" /> <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" /> </outputs> <tests> <test> <param name="seq_method_list" value="single-read"/> <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> <param name="genomeSource" value="history"/> <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/> <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/> <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/> </test> <test> <param name="seq_method_list" value="paired-end"/> <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/> <param name="input2_fastq" value="chrY-500k.R2.fastqsanger.gz" ftype="fastq.gz"/> <param name="genomeSource" value="history"/> <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/> <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/> <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/> <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/> <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/> </test> </tests> <help> **What it does** Reads are mapped to the genome using the Bowtie2 aligner. Reads mapping uniquely to the genome are assigned to subfamilies of repetitive elements based on their degree of overlap to RepeatMasker annotated genomic instances of each repetitive element subfamily. Reads mapping to multiple locations are separately mapped to repetitive element assemblies – referred to as repetitive element psuedogenomes – built from RepeatMasker annotated genomic instances of repetitive element subfamilies. RepEnrich then return tables of counts merged from both strategies, that can be further processed in statistical analysis for differential expression. For information on the method, see the `original publication`_. .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583 **Inputs** *Reference genome* : reference genome in fasta format *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format. *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from https://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html This file looks like: <![CDATA[ SW perc perc perc query position in query matching repeat position in repeat score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502 ]]> Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons) **Outputs** (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format for further statistical tests, differential expression analysis or graphics. **RepEnrich2** .. class:: warningmark the repenrich2 Galaxy wrapper was derived from the repenrich Galaxy wrapper repenrich2 uses bowtie2 for all alignment operations. We refer exclusively to our `GitHub repository`_ for code review. .. _GitHub repository: https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 **Execution time** .. class:: warningmark This tool includes time-consuming steps to index the reference genome, index repeat sequences and to align reads to these indexes. </help> <citations> <citation type="doi">10.1186/1471-2164-15-583</citation> </citations> </tool>