Mercurial > repos > florianbegusch > qiime2_suite_zmf
diff qiime2-2020.8/qiime_quality-control_filter-reads.xml @ 0:5c352d975ef7 draft
Uploaded
author | florianbegusch |
---|---|
date | Thu, 03 Sep 2020 09:33:04 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_quality-control_filter-reads.xml Thu Sep 03 09:33:04 2020 +0000 @@ -0,0 +1,110 @@ +<?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> \ No newline at end of file