Add Fairy #6647
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| name: Fairy | ||
| owner: iuc | ||
| description: Fast approximate contig coverage for metagenomic binning | ||
| homepage_url: https://github.com/bluenote-1577/fairy | ||
| long_description: | | ||
| Fairy is a software package, written in Rust, which create coverage file | ||
| for metagenomic binning. This tool can create coverage files 100x-1000x | ||
| faster than read alignment. | ||
| remote_repository_url: https://github.com/bluenote-1577/fairy | ||
| type: unrestricted | ||
| categories: | ||
| - Metagenomics |
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| <tool id="fairy_cov" name="Fairy coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>Create coverage file for specific binners</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
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| ln -s '$contig' '$contig.element_identifier' && | ||
| ln -s '$bcsp_file' '$bcsp_file.element_identifier' && | ||
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| fairy coverage | ||
| '$contig.element_identifier' | ||
| '$bcsp_file.element_identifier' | ||
| -t \${GALAXY_SLOTS:-8} | ||
|
There was a problem hiding this comment. Double quotes around bash variables are often a good idea. There was a problem hiding this comment. should have done if i did understand it correct |
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| -m ${minimum_ani} | ||
| -M ${min_number_kmers} | ||
| -c ${c} | ||
| -k ${k.value} | ||
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| --min-spacing ${min_spacing} | ||
| ${full_contig_name} | ||
| #if $output_type.value == 'semi': | ||
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There was a problem hiding this comment. Also here no You could simplify this, by using the command line parameter as value in the options and then just use There was a problem hiding this comment. Change it and there is no need for the value. I just forgot it to remove it since it did work with it |
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| --aemb-format | ||
| #end if | ||
| #if $output_type.value == 'max': | ||
| --maxbin-format | ||
| #end if | ||
| -o '$output' | ||
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| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="contig" type="data" format="fasta,fasta.gz" label="Input fasta contig file" help="Input the raw fasta contig file. It can be gzip!"/> | ||
| <param name="bcsp_file" type="data" format="bcsp" label="Input the pre-sketched file (.bcsp file)" help="This file will be generated with the fairy sketch tool."/> | ||
| <param argument="--minimum-ani" type="integer" optional="true" min="0" max="100" value="95" label="Set minimum ANI" help="Set the minimum adjusted ANI for the coverage calculation. CARE: only adjust it when you know what it does!"/> | ||
| <param argument="--min-number-kmers" type="integer" value="8" optional="true" label="Genome filter" help="Set the number for exclude genomes with less than this number of sampled k-mers."/> | ||
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There was a problem hiding this comment. Don't undersand this parameter. For the default sequences with less than 8 kmers are removed? There was a problem hiding this comment. I did rewrote this help, maybe it is better now to understand but yes this paramtere should be a filter to filter out genomes with less k-mers then this paramter There was a problem hiding this comment. I still do not understand this parameter. What does it mean if a genome has x k-mers? There was a problem hiding this comment. It means that a genome have less then x (the value of the parameter) k-mers it will execlude from the algorithm. It should not appear in the coverage file generated by Fairy. It this more cleare? And sorry for this missunderstanding There was a problem hiding this comment. Unfortunately no. I just do not understand what it means that a genome has a kmer. A genome of length n has n-k+1 kmers. There must be something special about the x kmers the help text is talking about. There was a problem hiding this comment. This x stands for a lower border to filter out genomes with less then x k-mers to not appear in the coverage file. For an example there are 3 genome in a contig. The first hast 5 k-mers, the second has 10 k-mers and the last one has 8 k-mers. We set this paramter to a 7 which means that the first genome with 5 k-mers will not be included since it hast less then 7 k-mers. When we set this to 2 then there will be no excluding of a genome since all 3 has more then 2 k-mers. Is this explenation better? |
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| <param argument="-c" type="integer" value="50" optional="true" label="Set subsampling rate" help="This value does not interact with the .bcsp file which was used as input."/> | ||
| <param argument="-k" type="select" label="Select k-mer size" help="This value does not interact with the .bcsp file which was used as input."> | ||
| <option value="31">31</option> | ||
| <option value="21">21</option> | ||
| </param> | ||
| <param argument="--min-spacing" type="integer" value="30" label="Set spacing between k-mers" help=" Minimum spacing between selected k-mers on the contigs."/> | ||
| <param argument="--full-contig-name" type="boolean" falsevalue="" truevalue="--full-contig-name" label="Full contig name"/> | ||
| <param name="output_type" type="select" label="Select for which binner the output should be generated"> | ||
| <option value="meta">MetaBAT2</option> | ||
| <option value="semi">SemiBin2</option> | ||
| <option value="max">MaxBin2</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="tabular" label="${tool.name} on ${on_string}"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/> | ||
| <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/> | ||
| <output name="output" value="normal_test.tsv"/> | ||
| </test> | ||
| <test> | ||
| <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/> | ||
| <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/> | ||
| <param name="minimum-ani" value="99"/> | ||
| <param name="min-number-kmers" value="2"/> | ||
| <param name="full-contig-name" value="true"/> | ||
| <param name="output_type" value="semi"/> | ||
| <output name="output" value="test_2.tsv"/> | ||
| </test> | ||
| <test> | ||
| <param name="contig" value="single_test.fasta.gz" ftype="fasta.gz"/> | ||
| <param name="bcsp_file" value="single_test.fasta.gz.bcsp" ftype="bcsp"/> | ||
| <param name="k" value="21"/> | ||
| <param name="c" value="45"/> | ||
| <param name="min-spacing" value="10"/> | ||
| <param name="output_type" value="max"/> | ||
| <output name="output" value="test_3.tsv"/> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
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| Fairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning. | ||
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| Fairy is used after metagenomic assembly and before binning. It can | ||
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| - Calculate coverage 100x-1000x faster than read alignment (e.g. BWA) | ||
| - Give comparable bins for multi-sample binning (short read or nanopore reads) | ||
| - Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more | ||
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| Caveats: | ||
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| - Don't use fairy for single-sample binning | ||
| - Don't use fairy for PacBio HiFi | ||
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| For more information visit `the wiki site on GitHub <https://github.com/bluenote-1577/fairy/wiki/Introduction-to-fairy>`_., | ||
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| .. class:: infomark | ||
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| Fairy usage for SemiBin2 is different than other tools: SemiBin2 requires separate coverage files for each read sample -- other tools require a single coverage matrix. | ||
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| .. class:: infomark | ||
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| The default output format from Fairy is the MetaBAT2 format. Any tool using this or the format from the other 2 binners work also with Fairys coverage files! | ||
| ]]> | ||
| </help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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| <tool id="fairy_sketch" name="Fairy sketch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | ||
| <description>sketching of k-mers for coverage into a hashtable</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
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| mkdir -p res && | ||
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| #if $input.is_select == "single": | ||
| #set $filename = $reads.element_identifier + '.bcsp' | ||
| ln -s '$reads' '$reads.element_identifier' && | ||
| #else | ||
| #set $filename = $first_pairs.element_identifier + '.paired.bcsp' | ||
| ln -s '$first_pairs' '$first_pairs.element_identifier' && | ||
| ln -s '$second_pairs' '$second_pairs.element_identifier' && | ||
| #end if | ||
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| fairy sketch | ||
| -t \${GALAXY_SLOTS:-8} | ||
| -c ${c} | ||
| -k ${k.value} | ||
| -d 'res' | ||
| #if $input.is_select == "single": | ||
| -r '$reads.element_identifier' | ||
| #else | ||
| -1 '$first_pairs.element_identifier' | ||
| -2 '$second_pairs.element_identifier' | ||
| #end if | ||
| && | ||
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| cp './res/${filename}' $output | ||
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| ]]> | ||
| </command> | ||
| <inputs> | ||
| <conditional name="input"> | ||
| <param name="is_select" type="select" label="Single or paired-end reads"> | ||
| <option value="single">Single</option> | ||
| <option value="pair">Paired</option> | ||
| </param> | ||
| <when value="single"> | ||
| <param argument="--reads" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input single-end reads"/> | ||
| </when> | ||
| <when value="pair"> | ||
| <param argument="--first_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input first paired-end reads"/> | ||
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There was a problem hiding this comment. I would prefer input as paired collection, at least add it as option. There was a problem hiding this comment. Add this option with a test! |
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| <param argument="--second_pairs" type="data" format="fastqsanger,fasta,fastq,fasta.gz,fastq.gz" label="Input second paired-end reads"/> | ||
| </when> | ||
| </conditional> | ||
| <param argument="-c" type="integer" value="50" optional="true" label="Set the subsampling rate"/> | ||
| <param argument="-k" type="select" label="Select k-mer size"> | ||
| <option value="31">31</option> | ||
| <option value="21">21</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="bcsp" label="${tool.name} on ${on_string}"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <conditional name="input"> | ||
| <param name="is_select" value="single"/> | ||
| <param name="reads" value="single_test.fasta.gz" ftype="fasta.gz"/> | ||
| </conditional> | ||
| <output name="output" file="single_test.fasta.gz.bcsp"/> | ||
| </test> | ||
| <test> | ||
| <conditional name="input"> | ||
| <param name="is_select" value="pair"/> | ||
| <param name="first_pairs" value="test_paired_1.fq.gz" ftype="fastq.gz"/> | ||
| <param name="second_pairs" value="test_paired_2.fq.gz" ftype="fastq.gz"/> | ||
| </conditional> | ||
| <output name="output" file="test_paired_1.fq.gz.paired.bcsp"/> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
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| This tool sketch the k-mer into a hashtable which will be needed for the fairy coverage tool to create the coverage file. | ||
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| .. class:: infomark | ||
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| This tool can either use single-end or paired-end reads as input in multiple file formats. | ||
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| Fairy can only handle a k-mer size of 31 or 21 not more or less currently! | ||
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| ]]> | ||
| </help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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| <macros> | ||
| <xml name="requirements"> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">fairy</requirement> | ||
| <yield/> | ||
| </requirements> | ||
| </xml> | ||
| <token name="@TOOL_VERSION@">0.5.7</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">24.1</token> | ||
| <xml name="citations"> | ||
| <citations> | ||
| <citation type="doi">10.1101/2024.04.23.590803</citation> | ||
| <yield/> | ||
| </citations> | ||
| </xml> | ||
| </macros> |
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| contigName contigLen totalAvgDepth single_test.fasta.gz single_test.fasta.gz-var | ||
| NZ_CP017438.1 3123040 0.05509718146076748 0.05509718146076748 0.014618167653679848 |
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| @@ -0,0 +1 @@ | ||
| NZ_CP017438.1 0.05509718146076748 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| contigName | ||
| NZ_CP017438.1 |
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It's not a good idea to just use the element identifiers, since they might contain dangerous or forbidden characters. We usually solve this like so
tools-iuc/tools/coverm/macros.xml
Line 55 in 295026b
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Did change it on both wrappers