Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml @ 20:d93d8888f0b0 draft
Uploaded
author | florianbegusch |
---|---|
date | Fri, 04 Sep 2020 12:44:24 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,119 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" + version="2020.8"> + <description>BLAST+ consensus taxonomy classifier</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime feature-classifier classify-consensus-blast + +--i-query=$iquery + +--i-reference-reads=$ireferencereads + +--i-reference-taxonomy=$ireferencetaxonomy + +--p-maxaccepts=$pmaxaccepts + +--p-perc-identity=$ppercidentity + +--p-query-cov=$pquerycov + +#if str($pstrand) != 'None': +--p-strand=$pstrand +#end if + +--p-evalue=$pevalue + +--p-min-consensus=$pminconsensus + +#if str($punassignablelabel): + --p-unassignable-label=$punassignablelabel +#end if +--o-classification=oclassification + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp oclassification.qza $oclassification + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data" /> + <param label="--p-maxaccepts: INTEGER Maximum number of hits to keep for each query. Must Range(1, None) be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query. [default: 10]" min="1" name="pmaxaccepts" optional="True" type="integer" value="10" /> + <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0]. [default: 0.8]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.8" /> + <param exclude_max="False" label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn\'s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0]. [default: 0.8]" max="1.0" min="0.0" name="pquerycov" optional="True" type="float" value="0.8" /> + <param label="--p-strand: " name="pstrand" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="both">both</option> + <option value="plus">plus</option> + <option value="minus">minus</option> + </param> + <param label="--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001" /> + <param exclude_max="False" exclude_min="True" label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" /> + <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" /> + <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}: classification.qza" name="oclassification" /> + + </outputs> + + <help><![CDATA[ +BLAST+ consensus taxonomy classifier +############################################################### + +Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local +alignment between query and reference_reads, then assigns consensus +taxonomy to each query sequence from among maxaccepts hits, min_consensus +of which share that taxonomic assignment. Note that maxaccepts selects the +first N hits with > perc_identity similarity to query, not the top N +matches. For top N hits, use classify-consensus-vsearch. + +Parameters +---------- +query : FeatureData[Sequence] + Sequences to classify taxonomically. +reference_reads : FeatureData[Sequence] + reference sequences. +reference_taxonomy : FeatureData[Taxonomy] + reference taxonomy labels. +maxaccepts : Int % Range(1, None), optional + Maximum number of hits to keep for each query. Must be in range [1, + infinity]. BLAST will choose the first N hits in the reference database + that exceed perc_identity similarity to query. +perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if percent identity to query is lower. Must be in range + [0.0, 1.0]. +query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional + Reject match if query alignment coverage per high-scoring pair is + lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not + behave identically to the query_cov parameter used by classify- + consensus-vsearch. Must be in range [0.0, 1.0]. +strand : Str % Choices('both', 'plus', 'minus'), optional + Align against reference sequences in forward ("plus"), reverse + ("minus"), or both directions ("both"). +evalue : Float, optional + BLAST expectation value (E) threshold for saving hits. +min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional + Minimum fraction of assignments must match top hit to be accepted as + consensus assignment. Must be in range (0.5, 1.0]. +unassignable_label : Str, optional + +Returns +------- +classification : FeatureData[Taxonomy] + Taxonomy classifications of query sequences. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file