Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_quality-filter_q-score-joined.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | a025a4a89e07 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_quality-filter_q-score-joined.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,81 @@ +<?xml version="1.0" ?> +<tool id="qiime_quality-filter_q-score-joined" name="qiime quality-filter q-score-joined" version="2019.4"> + <description> - Quality filter based on joined sequence quality scores.</description> + <requirements> + <requirement type="package" version="2019.4">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime quality-filter q-score-joined + +--i-demux=$idemux + +#if $pminquality: + --p-min-quality=$pminquality +#end if + +#if $pqualitywindow: + --p-quality-window=$pqualitywindow +#end if + +#if $pminlengthfraction: + --p-min-length-fraction=$pminlengthfraction +#end if + +#if $pmaxambiguous: + --p-max-ambiguous=$pmaxambiguous +#end if + +--o-filtered-sequences=ofilteredsequences +--o-filter-stats=ofilterstats +; +cp ofilteredsequences.qza $ofilteredsequences; +cp ofilterstats.qza $ofilterstats + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[JoinedSequencesWithQuality] The demultiplexed sequence data to be quality filtered. [required]" name="idemux" optional="False" type="data"/> + <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]" name="pminquality" optional="True" type="integer" value="4"/> + <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read. [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3"/> + <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length. [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75"/> + <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`. [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0"/> + </inputs> + <outputs> + <data format="qza" label="${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 joined sequence quality scores. +####################################################### + +This method filters joined sequence based on quality scores and the +presence of ambiguous base calls. + +Parameters +---------- +demux : SampleData[JoinedSequencesWithQuality] + 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[JoinedSequencesWithQuality] + 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>