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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabuli commit 4bb153f5820d234c08ea0f21e3e59938d1ab10b9
author | iuc |
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date | Tue, 04 Jun 2024 12:18:48 +0000 |
parents | b01d6b38f779 |
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<tool id="metabuli_classify" name="metabuli classify" version="@VERSION@+galaxy0" profile="20.01"> <description> metagenomic sequences </description> <macros> <import>macros.xml</import> </macros> <xrefs> <xref type="bio.tools">metabuli</xref> </xrefs> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ if [ -z "\$GALAXY_MEMORY_MB" ] ; then METABULI_GALAXY_MEMORY_GB=8 ; else METABULI_GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024) - 1) ; fi ; #set ext = '.fastq' #if str($library.lib_type) == "paired" #if $library.r1.ext.endswith('.gz'): #set ext = $ext + '.gz' #end if #set read1_file = 'r1' + $ext #set read2_file = 'r2' + $ext ln -s '$library.r1' $read1_file && ln -s '$library.r2' $read2_file && #else if str($library.lib_type) == "single" #if $library.single.ext.endswith('.gz'): #set ext = $ext + '.gz' #end if #set se_read = 'sr' + $ext ln -s '$library.single' $se_read && #else if str($library.lib_type) == "collection" #set ext = '.fastq' #if $library.input1.forward.ext.endswith('.gz'): #set ext = $ext + '.gz' #end if #set read1_file = 'r1' + $ext #set read2_file = 'r2' + $ext ln -s '$library.input1.forward' $read1_file && ln -s '$library.input1.reverse' $read2_file && #end if metabuli classify #if str($library.lib_type) == "paired" $read1_file $read2_file #else if str($library.lib_type) == "single" $se_read --mask $library.mask #else if str($library.lib_type) == "collection" $read1_file $read2_file #end if '$metabuli_databases.fields.path' out mtbl #if str($taxonomy_options.taxonomy_path) == 'local' --taxonomy-path '$taxonomy_options.taxonomy.fields.path' #end if --threads \${GALAXY_SLOTS:-4} --min-score $min_score --min-cov $min_cov --min-cons-cnt $min_cons_cnt --min-cons-cnt-euk $min_cons_cnt_euk --min-sp-score $min_sp_score --hamming-margin $hamming_margin --match-per-kmer $match_per_kmer #if $accession_level --accession-level 1 #end if #if str($library.lib_type) == "single" --seq-mode $library.seq_mode #end if --max-ram \${METABULI_GALAXY_MEMORY_GB:-8} > '$log' ]]> </command> <inputs> <conditional name="library"> <param name="lib_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> <option value="paired" selected="true">Paired End</option> <option value="single">Single End</option> <option value="collection">Paired Collection</option> </param> <when value="paired"> <param name="r1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> <param name="r2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> </when> <when value="single"> <param name="single" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Read" help="Single end/long read"/> <param name="seq_mode" type="select" label="Sequence Mode"> <option value="3" selected="true">Long Read</option> <option value="1">Single End Short Read</option> </param> <param argument="--mask" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Mask low complexity sequences in k-mer stage"/> </when> <when value="collection"> <param name="input1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> </when> </conditional> <!-- DATABASE INPUT--> <param label="Select a database" name="metabuli_databases" type="select"> <options from_data_table="metabuli_databases"> <validator message="No database is available" type="no_options" /> </options> </param> <conditional name="taxonomy_options"> <param name="taxonomy_path" type="select" label="Select taxonomy path from either local or accompanied metabuli db?"> <option value="local">Use a local taxonomy</option> <option value="embed" selected="true">Use one from a metabuli database</option> </param> <when value="local"> <param name="taxonomy" label="Select taxonomy" type="select"> <options from_data_table="taxonomy"> <validator message="No database is available" type="no_options" /> </options> </param> </when> <when value="embed"> </when> </conditional> <param argument="--min-score" type="float" min="0" max="1" value="0.000" label="Min sequence similarity score." help="Value for precision mode: ONT(0.008), PacBio Sequel II (0.005), PacBio HiFi (0.07), Illumina (0.15)"/> <param argument="--min-sp-score" type="float" min="0" max="1" value="0.0" label="Min. score for species-level or lower-level classification." help="Value for precision mode: PacBio HiFi (0.3), Illumina (0.5)"/> <param argument="--min-cov" type="float" min="0" max="1" value="0.0" label="Min query coverage."/> <param argument="--min-cons-cnt" type="integer" min="0" max="100" value="4" label="Min. number of consecutive matches for prokaryote/virus classification."/> <param argument="--min-cons-cnt-euk" type="integer" min="0" max="100" value="9" label="Min. number of consecutive matches for eukaryote classification."/> <param argument="--hamming-margin" type="integer" min="0" max="100" value="0" label="It allows extra Hamming distance than the minimum distance."/> <param argument="--match-per-kmer" type="integer" min="0" max="100" value="0" label="Num. of matches per query k-mer. Larger values assign more memory for storing k-mer matches."/> <param argument="--accession-level" type="boolean" truevalue="1" falsevalue="0" checked="false" label="search a database for accession-level classification."/> </inputs> <outputs> <data format="tabular" name="report" label="${tool.name} on ${on_string} report file" from_work_dir="out/mtbl_report.tsv" /> <data format="tabular" name="classification" label="${tool.name} on ${on_string}: classification" from_work_dir="out/mtbl_classifications.tsv"/> <data format="html" name="krona" label="${tool.name} on ${on_string}: Krona report" from_work_dir="out/mtbl_krona.html"/> <data format="txt" name="log" label="${tool.name} on ${on_string}: Log file"/> </outputs> <tests> <!-- PE Illumina --> <test expect_num_outputs="4"> <param name="lib_type" value="paired"/> <param name="r1" value="reads/illumina_R1.fastq.gz" ftype="fastqsanger.gz"/> <param name="r2" value="reads/illumina_R2.fastq.gz" ftype="fastqsanger.gz" /> <param name="metabuli_databases" value="RefSeqTest"/> <param name="taxonomy_path" value="local" /> <param name="taxonomy" value="taxonomy"/> <output name="report"> <assert_contents> <has_text text="Escherichia coli str. K-12 substr. MG1655"/> <has_text text="511145"/> <has_text text="66.6667"/> </assert_contents> </output> </test> <!-- Long read ONT --> <test expect_num_outputs="4"> <param name="lib_type" value="single"/> <param name="single" value="reads/ont.r10.4.1.fastq.gz" ftype="fastq.gz"/> <param name="metabuli_databases" value="RefSeqTest"/> <param name="taxonomy_path" value="local" /> <param name="taxonomy" value="taxonomy"/> <output name="report"> <assert_contents> <has_text text="Escherichia coli str. K-12 substr. MG1655"/> <has_text text="30.4348"/> </assert_contents> </output> </test> <!-- Long read ONT Precision mode --> <test expect_num_outputs="4"> <param name="lib_type" value="single"/> <param name="single" value="reads/ont.r10.4.1.fastq.gz" ftype="fastq.gz"/> <param name="min_score" value="0.008" /> <param name="metabuli_databases" value="RefSeqTest"/> <param name="taxonomy_path" value="local" /> <param name="taxonomy" value="taxonomy"/> <output name="report"> <assert_contents> <has_text text="21.7391"/> <has_text text="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"/> </assert_contents> </output> </test> <!-- Long read Pacbio HiFi --> <test expect_num_outputs="4"> <param name="lib_type" value="single"/> <param name="single" value="reads/pacbio.hifi.fastq.gz" ftype="fastq.gz"/> <param name="metabuli_databases" value="RefSeqTest"/> <param name="taxonomy_path" value="local" /> <param name="taxonomy" value="taxonomy"/> <output name="report"> <assert_contents> <has_text text="Salmonella enterica subsp. enterica serovar Typhimurium str. LT2"/> <has_text text="32.5000"/> </assert_contents> </output> <output name="classification"> <assert_contents> <has_text text="a4d8d18d-afde-b01a-d552-476bc9831614"/> <has_text text="208964:931"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ Metabuli_ specific and sensitive metagenomic classification via joint analysis of DNA and amino acid. .. _Metabuli: https://github.com/steineggerlab/Metabuli/tree/master?tab=readme-ov-file#classification ]]> </help> <expand macro="citations" /> </tool>