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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:46:48 +0000 |
parents | d93d8888f0b0 |
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<?xml version="1.0" ?> <tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score" version="2020.8"> <description>Quality filter based on sequence quality scores.</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime quality-filter q-score --i-demux=$idemux --p-min-quality=$pminquality --p-quality-window=$pqualitywindow --p-min-length-fraction=$pminlengthfraction --p-max-ambiguous=$pmaxambiguous --o-filtered-sequences=ofilteredsequences --o-filter-stats=ofilterstats #if str($examples) != 'None': --examples=$examples #end if ; cp ofilterstats.qza $ofilterstats ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data" /> <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4" /> <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3" /> <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75" /> <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0" /> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" /> <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats" /> </outputs> <help><![CDATA[ Quality filter based on sequence quality scores. ############################################################### This method filters sequence based on quality scores and the presence of ambiguous base calls. Parameters ---------- demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The demultiplexed sequence data to be quality filtered. min_quality : Int, optional The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. quality_window : Int, optional The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. min_length_fraction : Float, optional The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. max_ambiguous : Int, optional The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min_length_fraction`. Returns ------- filtered_sequences : SampleData[SequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The resulting quality-filtered sequences. filter_stats : QualityFilterStats Summary statistics of the filtering process. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>