Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-classifier_classify-consensus-blast.xml @ 14:a0a8d77a991c draft
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| author | florianbegusch |
|---|---|
| date | Thu, 03 Sep 2020 09:51:29 +0000 |
| parents | f190567fe3f6 |
| children |
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--- a/qiime2/qiime_feature-classifier_classify-consensus-blast.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_feature-classifier_classify-consensus-blast.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,105 +1,74 @@ <?xml version="1.0" ?> -<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast" version="2019.7"> - <description> - BLAST+ consensus taxonomy classifier</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<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 -#if str( $id_to_taxonomy_fp.selector ) == 'history' -#set $tax = $id_to_taxonomy_fp.taxonomy_fp ---i-reference-taxonomy '$tax' -#else: -#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path ---i-reference-taxonomy '$tax' -#end if +--i-reference-taxonomy=$ireferencetaxonomy + +--p-maxaccepts=$pmaxaccepts +--p-perc-identity=$ppercidentity -#if str($pmaxaccepts): - --p-maxaccepts=$pmaxaccepts -#end if +--p-query-cov=$pquerycov -#if str($ppercidentity): - --p-perc-identity=$ppercidentity +#if str($pstrand) != 'None': +--p-strand=$pstrand #end if -#if str($pquerycov): - --p-query-cov=$pquerycov -#end if - -#if str($pstrand) != 'None': - --p-strand=$pstrand -#end if - -#if str($pevalue): - --p-evalue=$pevalue -#end if +--p-evalue=$pevalue -#if str($pminconsensus): - --p-min-consensus=$pminconsensus -#end if - - - - - -#if '__sq__' in str($punassignablelabel): - #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'") - #set $punassignablelabel = $punassignablelabel_temp -#end if +--p-min-consensus=$pminconsensus #if str($punassignablelabel): - --p-unassignable-label="$punassignablelabel" + --p-unassignable-label=$punassignablelabel +#end if +--o-classification=oclassification + +#if str($examples) != 'None': +--examples=$examples #end if - - ---o-classification=oclassification ; 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"/> - - <conditional name="id_to_taxonomy_fp" optional="True"> - <param name="selector" type="select" label="Reference taxonomy to query"> - <option value="cached">Public databases</option> - <option value="history">Databases from your history</option> - </param> - <when value="cached"> - <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> - <options from_data_table="qiime_taxonomy" /> - </param> - </when> - <when value="history"> - <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> - </when> - </conditional> - <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]" name="pmaxaccepts" optional="True" type="integer" min="1" value="10"/> - <param 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]" name="ppercidentity" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.8"/> - <param 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]" name="pquerycov" optional="True" min="0" max="1" exclude_max="False" 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 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]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/> - <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/> - </inputs> - <outputs> - <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> - </outputs> - <help><![CDATA[ + ]]></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 @@ -137,15 +106,14 @@ 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> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file