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view qiime2/qiime_quality-control_filter-reads.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
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<?xml version="1.0" ?> <tool id="qiime_quality-control_filter-reads" name="qiime quality-control filter-reads" version="2020.8"> <description>Filter demultiplexed sequences by alignment to reference database.</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-control filter-reads --i-demultiplexed-sequences=$idemultiplexedsequences --i-database=$idatabase --p-n-threads=$pnthreads #if str($pmode) != 'None': --p-mode=$pmode #end if #if str($psensitivity) != 'None': --p-sensitivity=$psensitivity #end if --p-ref-gap-open-penalty=$prefgapopenpenalty --p-ref-gap-ext-penalty=$prefgapextpenalty #if $pnoexcludeseqs: --p-no-exclude-seqs #end if --o-filtered-sequences=ofilteredsequences #if str($examples) != 'None': --examples=$examples #end if ; cp ofilteredsequences.qza $ofilteredsequences ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" /> <param format="qza,no_unzip.zip" label="--i-database: ARTIFACT Bowtie2 indexed database. Bowtie2Index [required]" name="idatabase" optional="False" type="data" /> <param label="--p-mode: " name="pmode" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="local">local</option> <option value="global">global</option> </param> <param label="--p-sensitivity: " name="psensitivity" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="very-fast">very-fast</option> <option value="fast">fast</option> <option value="sensitive">sensitive</option> <option value="very-sensitive">very-sensitive</option> </param> <param label="--p-ref-gap-open-penalty: INTEGER Range(1, None) Reference gap open penalty. [default: 5]" min="1" name="prefgapopenpenalty" optional="True" type="integer" value="5" /> <param label="--p-ref-gap-ext-penalty: INTEGER Range(1, None) Reference gap extend penalty. [default: 3]" min="1" name="prefgapextpenalty" optional="True" type="integer" value="3" /> <param label="--p-no-exclude-seqs: Do not exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. [default: True]" name="pnoexcludeseqs" selected="False" type="boolean" /> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" /> </outputs> <help><![CDATA[ Filter demultiplexed sequences by alignment to reference database. ############################################################### Filter out (or keep) demultiplexed single- or paired-end sequences that align to a reference database, using bowtie2 and samtools. This method can be used to filter out human DNA sequences and other contaminants in any FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or alternatively (when exclude_seqs is False) to only keep sequences that do align to the reference. Parameters ---------- demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed. database : Bowtie2Index Bowtie2 indexed database. n_threads : Int % Range(1, None), optional Number of alignment threads to launch. mode : Str % Choices('local', 'global'), optional Bowtie2 alignment settings. See bowtie2 manual for more details. sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional Bowtie2 alignment sensitivity. See bowtie2 manual for details. ref_gap_open_penalty : Int % Range(1, None), optional Reference gap open penalty. ref_gap_ext_penalty : Int % Range(1, None), optional Reference gap extend penalty. exclude_seqs : Bool, optional Exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database. Returns ------- filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The resulting filtered sequences. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>