Mercurial > repos > florianbegusch > qiime2_suite
view qiime2/qiime_taxa_collapse.xml @ 10:21c7954105a9 draft
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author | florianbegusch |
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date | Sun, 25 Aug 2019 10:26:27 -0400 |
parents | f190567fe3f6 |
children | a0a8d77a991c |
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<?xml version="1.0" ?> <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.7"> <description> - Collapse features by their taxonomy at the specified level</description> <requirements> <requirement type="package" version="2019.7">qiime2</requirement> </requirements> <command><![CDATA[ qiime taxa collapse #if str( $id_to_taxonomy_fp.selector ) == 'history' #set $tax = $id_to_taxonomy_fp.taxonomy_fp --i-taxonomy '$tax' #else: #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path --i-taxonomy '$tax' #end if --i-table=$itable #if str($plevel): --p-level="$plevel" #end if --o-collapsed-table=ocollapsedtable ; cp ocollapsedtable.qza $ocollapsedtable ]]></command> <inputs> <conditional name="id_to_taxonomy_fp" optional="True"> <param name="selector" type="select" label="Reference taxonomy to query"> <option value="cached">Public databases</option> <option value="history">Databases from your history</option> </param> <when value="cached"> <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> <options from_data_table="qiime_taxonomy" /> </param> </when> <when value="history"> <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> </when> </conditional> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/> <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/> </outputs> <help><![CDATA[ Collapse features by their taxonomy at the specified level ########################################################## Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. Parameters ---------- table : FeatureTable[Frequency] Feature table to be collapsed. taxonomy : FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. level : Int The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. Returns ------- collapsed_table : FeatureTable[Frequency] The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>