Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_quality-filter_q-score.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_quality-filter_q-score.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,85 @@ +<?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> \ No newline at end of file