Mercurial > repos > galaxy-australia > kmc
view kmc_tools_filter.xml @ 2:c97f8a687258 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
author | galaxy-australia |
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date | Wed, 02 Oct 2024 08:34:43 +0000 |
parents | c7fda6e88567 |
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<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>filtering KMC's database</description> <xrefs> <xref type='bio.tools'>kmc</xref> </xrefs> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ #for $f in $input_collection: #if '.kmc_suf' in str($f.element_identifier) ln -s '${f}' db.kmc_suf && #else ln -s '${f}' db.kmc_pre && #end if #end for kmc_tools filter -t\${GALAXY_SLOTS:-2} #if $t: '$t' #end if #if $hm: '$hm' #end if db -ci'$min_kmer_occurrence' -cx'$max_kmer_occurrence' $input_read_file -f'$input_format' -ci'$exclude_length' -cx'$exclude_kmer_occurence' #if str($output_format) == 'q': $filter_output_fastq #else $filter_output_fasta #end if -f'$output_format' ]]></command> <inputs> <param name="input_collection" type="data_collection" collection_type="list" label="KMC db"/> <param name="input_read_file" type="data" format="fastq,fasta" label="input read file" help="Input file format FASTQ/FASTA [default:FASTQ]"/> <expand macro="input_option"/> <param name="input_format" argument="-f" type="select" label="input read file format [default:FASTQ]"> <option value="q" selected="true">FASTQ</option> <option value="a">FASTA</option> </param> <param argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="trim reads" help="trim reads on first invalid k-mer instead of remove entirely"/> <param argument="-hm" type="boolean" truevalue="-hm" falsevalue="" checked="false" label="hard mask" help="hard mask invalid k-mers in a read"/> <expand macro="general_option"/> <param name="output_format" argument="-f" type="select" label="output read file format [default:FASTQ]"> <option value="q" selected="true">FASTQ</option> <option value="a">FASTA</option> </param> </inputs> <outputs> <data name="filter_output_fastq" format="fastq" label="${tool.name} on ${on_string}: filter"> <filter>'q' in output_format</filter> </data> <data name="filter_output_fasta" format="fasta" label="${tool.name} on ${on_string}: filter"> <filter>'a' in output_format</filter> </data> </outputs> <tests> <test> <!-- #1 test with common parameters --> <param name="input_collection"> <collection type="list"> <element name="db.kmc_pre" value="filtered_kmers1.kmc_pre" dbkey="89"/> <element name="db.kmc_suf" value="filtered_kmers1.kmc_suf" dbkey="89"/> </collection> </param> <param name="input_read_file" value="Illumina.1.fastq" ftype="fastq"/> <param name="min_kmer_occurrence" value="3" /> <param name="exclude_length" value="2" /> <param name="exclude_kmer_occurence" value="10" /> <output name="filtered_1.fastq" file="filtered_1.fastq" ftype="fastq" /> </test> <test> <!-- #2 test with common parameters --> <param name="input_collection"> <collection type="list"> <element name="db.kmc_pre" value="filtered_kmers2.kmc_pre" dbkey="89"/> <element name="db.kmc_suf" value="filtered_kmers2.kmc_suf" dbkey="89"/> </collection> </param> <param name="input_read_file" value="Illumina.2.fastq" ftype="fastq"/> <param name="exclude_length" value="10" /> <param name="exclude_kmer_occurence" value="100" /> <output name="filtered_2.fastq" file="filtered_2.fastq" ftype="fastq" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** *K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.* **Input** - input file - FASTA, FASTQ and BAM. Also, gipped versions of FASTA and FASTQ. **Command line Example:** - kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered_1.fastq - kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered_2.fastq **Output** - filtered_1.fastq - filtered_2.fastq .. class:: infomark **References** More information are available on `website <http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about>`_. ]]></help> <citations> <citation type="doi">DOI: 10.1093/bioinformatics/btx304</citation> <citation type="doi">DOI: 10.1093/bioinformatics/btv022</citation> <citation type="doi">DOI: 10.1186/1471-2105-14-160</citation> </citations> </tool>