Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_vsearch_join-pairs.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_vsearch_join-pairs.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,137 @@ +<?xml version="1.0" ?> +<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" + version="2020.8"> + <description>Join paired-end reads.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime vsearch join-pairs + +--i-demultiplexed-seqs=$idemultiplexedseqs + +#if str($ptruncqual): + --p-truncqual=$ptruncqual +#end if +--p-minlen=$pminlen + +#if str($pmaxns): + --p-maxns=$pmaxns +#end if +#if $pallowmergestagger: + --p-allowmergestagger +#end if + +--p-minovlen=$pminovlen + +--p-maxdiffs=$pmaxdiffs + +#if str($pminmergelen): + --p-minmergelen=$pminmergelen +#end if +#if str($pmaxmergelen): + --p-maxmergelen=$pmaxmergelen +#end if +#if str($pmaxee): + --p-maxee=$pmaxee +#end if +--p-qmin=$pqmin + +--p-qminout=$pqminout + +--p-qmax=$pqmax + +--p-qmaxout=$pqmaxout + +--p-threads=$pthreads + +--o-joined-sequences=ojoinedsequences + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ojoinedsequences.qza $ojoinedsequences + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data" /> + <param label="--p-truncqual: INTEGER Truncate sequences at the first base with the Range(0, None) specified quality score value or lower. [optional]" name="ptruncqual" optional="False" type="text" /> + <param label="--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]" min="0" name="pminlen" optional="True" type="integer" value="1" /> + <param label="--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]" name="pmaxns" optional="False" type="text" /> + <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" /> + <param label="--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]" min="0" name="pminovlen" optional="True" type="integer" value="10" /> + <param label="--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]" min="0" name="pmaxdiffs" optional="True" type="integer" value="10" /> + <param label="--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="False" type="text" /> + <param label="--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="False" type="text" /> + <param label="--p-maxee: NUMBER Maximum number of expected errors in the joined read Range(0.0, None) to be retained. [optional]" name="pmaxee" optional="False" type="text" /> + <param exclude_max="False" label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" max="2" min="-5" name="pqmin" optional="True" type="integer" value="0" /> + <param exclude_max="False" label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" max="2" min="-5" name="pqminout" optional="True" type="integer" value="0" /> + <param exclude_max="False" label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" max="41" min="40" name="pqmax" optional="True" type="integer" value="41" /> + <param exclude_max="False" label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" max="41" min="40" name="pqmaxout" optional="True" type="integer" value="41" /> + <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}: joinedsequences.qza" name="ojoinedsequences" /> + + </outputs> + + <help><![CDATA[ +Join paired-end reads. +############################################################### + +Join paired-end sequence reads using vsearch's merge_pairs function. The +qmin, qminout, qmax, and qmaxout parameters should only need to be modified +when working with older fastq sequence data. See the vsearch documentation +for details on how paired-end joining is performed, and for more +information on the parameters to this method. + +Parameters +---------- +demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality] + The demultiplexed paired-end sequences to be joined. +truncqual : Int % Range(0, None), optional + Truncate sequences at the first base with the specified quality score + value or lower. +minlen : Int % Range(0, None), optional + Sequences shorter than minlen after truncation are discarded. +maxns : Int % Range(0, None), optional + Sequences with more than maxns N characters are discarded. +allowmergestagger : Bool, optional + Allow joining of staggered read pairs. +minovlen : Int % Range(0, None), optional + Minimum overlap length of forward and reverse reads for joining. +maxdiffs : Int % Range(0, None), optional + Maximum number of mismatches in the forward/reverse read overlap for + joining. +minmergelen : Int % Range(0, None), optional + Minimum length of the joined read to be retained. +maxmergelen : Int % Range(0, None), optional + Maximum length of the joined read to be retained. +maxee : Float % Range(0.0, None), optional + Maximum number of expected errors in the joined read to be retained. +qmin : Int % Range(-5, 2, inclusive_end=True), optional + The minimum allowed quality score in the input. +qminout : Int % Range(-5, 2, inclusive_end=True), optional + The minimum allowed quality score to use in output. +qmax : Int % Range(40, 41, inclusive_end=True), optional + The maximum allowed quality score in the input. +qmaxout : Int % Range(40, 41, inclusive_end=True), optional + The maximum allowed quality score to use in output. +threads : Int % Range(0, 8, inclusive_end=True), optional + The number of threads to use for computation. Does not scale much past + 4 threads. + +Returns +------- +joined_sequences : SampleData[JoinedSequencesWithQuality] + The joined sequences. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file