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

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

--i-sequences=$isequences


#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-sequences=ofilteredsequences
;
cp ofilteredsequences.qza $ofilteredsequences
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] Feature sequences to be filtered.         [required]" name="isequences" 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 sequences. 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 sequences. 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}: filteredsequences.qza" name="ofilteredsequences"/>
	</outputs>
	<help><![CDATA[
Taxonomy-based feature sequence filter.
#######################################

This method filters sequences based on their taxonomic annotations.
Features can be retained in the result by specifying one or more include
search terms, and can be filtered out of the result 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.

Parameters
----------
sequences : FeatureData[Sequence]
    Feature sequences to be filtered.
taxonomy : FeatureData[Taxonomy]
    Taxonomic annotations for features in the provided feature sequences.
    All features in the feature sequences must have a corresponding
    taxonomic annotation. Taxonomic annotations for features that are not
    present in the feature sequences will be ignored.
include : Str, optional
    One or more search terms that indicate which taxa should be included in
    the resulting sequences. 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 sequences. 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_sequences : FeatureData[Sequence]
    The taxonomy-filtered feature sequences.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>