annotate qiime2/qiime_taxa_filter-table.xml @ 5:a025a4a89e07 draft

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<?xml version="1.0" ?>
<tool id="qiime_taxa_filter-table" name="qiime taxa filter-table" version="2019.4">
	<description> - Taxonomy-based feature table filter.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime taxa filter-table

--i-table=$itable


#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


#if str($pinclude):
 --p-include="$pinclude"
#end if

#if str($pexclude):
 --p-exclude="$pexclude"
#end if

#if str($pquerydelimiter):
 --p-query-delimiter="$pquerydelimiter"
#end if

#if str($pmode) != 'None':
 --p-mode=$pmode
#end if

--o-filtered-table=ofilteredtable
;
cp ofilteredtable.qza $ofilteredtable
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be filtered.              [required]" name="itable" 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-include: TEXT       One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.        [optional]" name="pinclude" optional="True" type="text"/>
		<param label="--p-exclude: TEXT       One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.         [optional]" name="pexclude" optional="True" type="text"/>
		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']" name="pquerydelimiter" optional="True" type="text" value=","/>
		<param label="--p-mode: " name="pmode" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="exact">exact</option>
			<option value="contains">contains</option>
		</param>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
	</outputs>
	<help><![CDATA[
Taxonomy-based feature table filter.
####################################

This method filters features from a table based on their taxonomic
annotations. Features can be retained in the resulting table by specifying
one or more include search terms, and can be filtered out of the resulting
table by specifying one or more exclude search terms. If both include and
exclude are provided, the inclusion critera will be applied before the
exclusion critera. Either include or exclude terms (or both) must be
provided. Any samples that have a total frequency of zero after filtering
will be removed from the resulting table.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to be filtered.
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 for features that are not present in
    the feature table will be ignored.
include : Str, optional
    One or more search terms that indicate which taxa should be included in
    the resulting table. If providing more than one term, terms should be
    delimited by the query-delimiter character. By default, all taxa will
    be included.
exclude : Str, optional
    One or more search terms that indicate which taxa should be excluded
    from the resulting table. If providing more than one term, terms should
    be delimited by the query-delimiter character. By default, no taxa will
    be excluded.
query_delimiter : Str, optional
    The string used to delimit multiple search terms provided to include or
    exclude. This parameter should only need to be modified if the default
    delimiter (a comma) is used in the provided taxonomic annotations.
mode : Str % Choices('exact', 'contains'), optional
    Mode for determining if a search term matches a taxonomic annotation.
    "contains" requires that the annotation has the term as a substring;
    "exact" requires that the annotation is a perfect match to a search
    term.

Returns
-------
filtered_table : FeatureTable[Frequency]
    The taxonomy-filtered feature table.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>