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| categories: | ||
| - Statistics | ||
| description: rdeval is a General purpose, multithreaded read analysis and manipulation tool. | ||
| homepage_url: https://github.com/vgl-hub/rdeval | ||
| long_description: | | ||
| rdeval is a single, fast and exhaustive tool for summary statistics | ||
| and simultaneous manipulation of sequence read files in fa*[.gz], | ||
| bam, and cram formats. rdeval also allows seamless file conversion | ||
| between formats. | ||
| name: rdeval | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/rdeval | ||
| type: unrestricted |
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| <macros> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">rdeval</requirement> | ||
| </requirements> | ||
| </xml> | ||
| <token name="@TOOL_VERSION@">0.0.5</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">23.02</token> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1101/2025.02.01.636073</citation> | ||
| </citations> | ||
| </xml> | ||
| </macros> |
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| <tool id="rdeval" name="rdeval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>Multithreaded read analysis and manipulation tool</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| #import re | ||
| #set $mangled_inputs = [] | ||
| #for $input in $input_reads | ||
| #set $mangled_base = re.sub(r"[^\w\-\s]", "_", str($input.element_identifier)) | ||
| #set $mangled_input = $mangled_base + "." + str($input.ext) | ||
| #silent $mangled_inputs.append($mangled_input) | ||
| ln -s '$input' '$mangled_input' && | ||
| #end for | ||
| #if $output_options.output_type.type_selector == "combined_reads" | ||
| ln -s '$reads_outfile' 'output.${output_type.format_selector}' && | ||
| #end if | ||
| rdeval --input-reads #echo " ".join([f"'{input}'" for $input in $mangled_inputs]) | ||
| #if $expected_gsize | ||
| $expected_gsize | ||
| #end if | ||
| #if $input_filter.filter_selector == "exclude_file" | ||
| --exclude-list '$exclude_file' | ||
| #else if $input_filter.filter_selector == "include_file" | ||
| --include-list '$include_file' | ||
| #end if | ||
| #if $filter | ||
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| --filter '$filter' | ||
| #end if | ||
| --sample '$sample' | ||
| #if $random_seed | ||
| --random-seed '$random_seed' | ||
| #end if | ||
| #if $homopolymer_compress | ||
| --homopolymer-compress '$homopolymer_compress' | ||
| #end if | ||
| #if $stats_flavor.flavor_selector == "stats" | ||
| $sequence_report | ||
| #else if $stats_flavor.flavor_selector == "quality" | ||
| --quality '$quality' | ||
| #else if $stats_flavor.flavor_selector == "size" | ||
| --out-size '$out_size' | ||
| #end if | ||
| #if $output_options.output_type.type_selector == "rd_file" | ||
| $md5 | ||
| -o output.rd | ||
| #else if $output_options.output_type.type_selector == "combined_reads" | ||
| -o 'output.${output_type.format_selector}' | ||
| #end if | ||
| $verbose | ||
| --tabular | ||
| --threads \${GALAXY_SLOTS:-2} | ||
| > '$stats_outfile' | ||
| ]]></command> | ||
| <inputs> | ||
| <param argument="--input-reads" type="data" format="bam,cram,fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input dataset" help="FASTA/FASTQ, BAM, or CRAM files."/> | ||
| <param name="expected_gsize" type="integer" min="0" optional="true" label="Expected Genome Size" help="Integer (e.g., 3000000000 for human)."/> | ||
| <section name="input_filter" title="Filter input reads" expanded="false"> | ||
| <conditional name="file_filter"> | ||
| <param name="filter_selector" type="select" label="Use an exclude or include file"> | ||
| <option value="no_file" selected="true">no</option> | ||
| <option value="exclude_file">Use an exclude file</option> | ||
| <option value="include_file">Use an include file</option> | ||
| </param> | ||
| <when value="no_file"/> | ||
| <when value="exclude_file"> | ||
| <param argument="--exclude-list" type="data" format="txt" optional="true" label="File containing headers to exclude"/> | ||
|
There was a problem hiding this comment. Optional makes no sense in the conditional. Maybe skip the conditional and just have the two parameters as optional? |
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| </when> | ||
| <when value="include_file"> | ||
| <param argument="--include-list" type="data" format="txt" optional="true" label="File containing headers to include"/> | ||
| </when> | ||
| </conditional> | ||
| <param argument="--filter" type="text" optional="true" label="filter" help="e.g. l>1000 & q>20"/> | ||
|
There was a problem hiding this comment. Unclear. Should we really offer it this way too users? |
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| </section> | ||
| <section name="input_subsample" title="Subsample input reads" expanded="false"> | ||
| <param argument="--sample" type="float" min="0" max="1" value="1" label="fraction of reads to subsample"/> | ||
| <param argument="--random-seed" type="integer" min="0" optional="true" label="random seed to make subsampling reproducible"/> | ||
| <param argument="--homopolymer-compress" type="integer" min="0" optional="true" label="Compress homopolymers longer than n in the input"/> | ||
|
There was a problem hiding this comment. What does this mean? |
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| </section> | ||
| <section name="output_options" title="Output options"> | ||
| <conditional name="stats_flavor"> | ||
| <param name="flavor_selector" type="select" label="Stats output"> | ||
| <option value="stats" selected="true">Stats</option> | ||
| <option value="quality">Quality</option> | ||
| <option value="size">Size</option> | ||
| </param> | ||
| <when value="stats"> | ||
| <param argument="--sequence-report" type="boolean" checked="false" truevalue="--sequence-report" falsevalue="" label="Per read sequence report"/> | ||
| </when> | ||
| <when value="quality"> | ||
| <param argument="--quality" type="select" optional="true" label="quality type"> | ||
| <option value="q" selected="true">Average quality for each read</option> | ||
| <option value="a">Both length and quality for each read</option> | ||
| </param> | ||
| </when> | ||
| <when value="size"> | ||
| <param argument="--out-size" type="select" optional="true" label="size list type"> | ||
|
There was a problem hiding this comment. Not sure what these options mean? |
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| <option value="u" selected="true">unsorted</option> | ||
| <option value="s">sorted</option> | ||
| <option value="h">histogram</option> | ||
| <option value="c">inverse cumulative table</option> | ||
| </param> | ||
| </when> | ||
| </conditional> | ||
| <conditional name="output_type"> | ||
| <param name="type_selector" type="select" label="output type"> | ||
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| <option value="rd_file" selected="true">RD file</option> | ||
| <option value="combined_reads">Combined reads</option> | ||
| </param> | ||
| <when value="combined_reads"> | ||
| <param name="format_selector" type="select" optional="true" label="Output format"> | ||
| <option value="fasta.gz" selected="true">fasta</option> | ||
| <option value="fastq.gz">fastq</option> | ||
| <option value="bam">bam</option> | ||
| <option value="cram">cram</option> | ||
| </param> | ||
| </when> | ||
| <when value="rd_file"> | ||
| <param argument="--md5" type="boolean" checked="false" truevalue="--md5" falsevalue="" label="Print md5 of .rd files"/> | ||
| </when> | ||
| </conditional> | ||
| <param argument="--verbose" type="boolean" checked="false" truevalue="--verbose" falsevalue="" label="Verbose output"/> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="stats_outfile" format="tabular" label="Rdeval summary"/> | ||
| <data name="rd_outfile" from_work_dir="output.rd" format="binary" label="RD File"> | ||
|
There was a problem hiding this comment. What kind of format is that? Will it be used by downstream tools? |
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| <filter>output_options["output_type"]["type_selector"] == "rd_file"</filter> | ||
| </data> | ||
| <data name="reads_outfile" format="binary" label="Output reads"> | ||
| <filter>output_options["output_type"]["type_selector"] == "combined_reads"</filter> | ||
| <change_format> | ||
| <when input="format_selector" value="fasta.gz" format="fasta.gz"/> | ||
| <when input="format_selector" value="fastq.gz" format="fastq.gz"/> | ||
| <when input="format_selector" value="bam" format="bam"/> | ||
|
There was a problem hiding this comment. This allows conversion from fasta to bam? |
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| <when input="format_selector" value="cram" format="cram"/> | ||
| </change_format> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_reads" value="test1.fasta.gz" ftype="fasta.gz"/> | ||
| <output name="stats_outfile" file="output1.tabular" ftype="tabular"/> | ||
| <output name="rd_outfile" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="109" delta="1"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_reads" value="test1.fastq.gz" ftype="fastq.gz"/> | ||
| <output name="stats_outfile" file="output1.tabular" ftype="tabular" lines_diff="2"/> | ||
| <output name="rd_outfile" ftype="binary"> | ||
| <assert_contents> | ||
| <has_size size="128" delta="1"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <test expect_num_outputs="2"> | ||
| <param name="input_reads" value="test2.bam" ftype="bam"/> | ||
| <param name="type_selector" value="combined_reads"/> | ||
| <output name="stats_outfile" file="output2.tabular" ftype="tabular"/> | ||
| <param name="format_selector" value="fastq.gz"/> | ||
| <output name="reads_outfile" file="output2.fastq.gz" ftype="fastq.gz"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
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| **rdeval** is a general-purpose, multithreaded tool for analyzing and manipulating reads (FASTA/FASTQ/BAM/CRAM/RD). | ||
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| rdeval input.fa*[.gz]|bam|cram|rd [expected genome size] | ||
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| :: | ||
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| Dataset report example: | ||
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| +++Read summary+++: | ||
| # reads: 10000 | ||
| Total read length: 134014104 | ||
| Average read length: 13401.41 | ||
| Read N50: 14270 | ||
| Smallest read length: 1142 | ||
| Largest read length: 40910 | ||
| Coverage: inf | ||
| GC content %: 43.78 | ||
| Base composition (A:C:T:G): 37693226:29331833:37655925:29333120 | ||
| Average per base quality: 26.47 | ||
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| :: | ||
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| Per sequence/read report (--sequence-report) example: | ||
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| Header Comment Length A C G T N GC Average Quality | ||
| m54306U_210528_154706/69206614/ccs 22812 6170 5146 4802 6694 0 0.44 89.9705 | ||
| m54306U_210528_154706/25888573/ccs 32200 9162 7270 7112 8656 0 0.45 56.8306 | ||
| m54306U_210528_154706/40634168/ccs 8487 2443 1858 1876 2310 0 0.44 90.3828 | ||
| m54306U_210528_154706/103745617/ccs 16496 4546 3752 3760 4438 0 0.46 88.3554 | ||
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| **Attribution** | ||
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| This tool relies on the gfastar suite and the gfalibs toolkit `vgl-hub/gfalibs <https://github.com/vgl-hub/gfalibs>`_, developed by Giulio Formenti at the Rockefeller University | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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| # reads 5 | ||
| Total read length 50 | ||
| Average read length 10.00 | ||
| Read N50 15 | ||
| Smallest read length 5 | ||
| Largest read length 15 | ||
| Coverage inf | ||
| GC content % 50.00 | ||
| Base composition (A:C:T:G) 9:14:11:6 | ||
| Average per base quality 0.00 |
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| # reads 11 | ||
| Total read length 264855 | ||
| Average read length 24077.73 | ||
| Read N50 24322 | ||
| Smallest read length 17465 | ||
| Largest read length 36274 | ||
| Coverage inf | ||
| GC content % 40.81 | ||
| Base composition (A:C:T:G) 79479:54455:77277:53644 | ||
| Average per base quality 23.58 |
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Description is quiet technical and at the same time non descriptive.