Mercurial > repos > galaxy-australia > kmc
diff kmc_tools_filter.xml @ 0:ca2743037241 draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 29b98036c21809c923a92feb38b736c007d2e303"
author | galaxy-australia |
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date | Tue, 27 Sep 2022 05:20:06 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kmc_tools_filter.xml Tue Sep 27 05:20:06 2022 +0000 @@ -0,0 +1,134 @@ +<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > + <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_suf" value="db.kmc_suf" dbkey="89"/> + <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> + </collection> + </param> + <param name="input_read_file" value="F3D0_R1.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_suf" value="db.kmc_suf" dbkey="89"/> + <element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/> + </collection> + </param> + <param name="input_read_file" value="F3D0_R1.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>