<?xml version="1.0" ?>
<tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features" version="2019.4">
	<description> - Filter fragments in tree from table.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime fragment-insertion filter-features

--i-table=$itable
--i-tree=$itree

--o-filtered-table=ofilteredtable
--o-removed-table=oremovedtable
;
cp ofilteredtable.qza $ofilteredtable;
cp oremovedtable.qza $oremovedtable
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run.                    [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    The tree resulting from inserting fragments into a Phylogeny[Rooted]  reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
		<data format="qza" label="${tool.name} on ${on_string}: removedtable.qza" name="oremovedtable"/>
	</outputs>
	<help><![CDATA[
Filter fragments in tree from table.
####################################

Filters fragments not inserted into a phylogenetic tree from a feature-
table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
get inserted by SEPP into a reference phylogeny. To be able to use the
feature-table for downstream analyses like computing Faith's PD or UniFrac,
the feature-table must be cleared of fragments that are not part of the
phylogenetic tree, because their path length can otherwise not be
determined. Typically, the number of rejected fragments is low (<= 10), but
it might be worth to inspect the ratio of reads assigned to those rejected
fragments.

Parameters
----------
table : FeatureTable[Frequency]
    A feature-table which needs to filtered down to those fragments that
    are contained in the tree, e.g. result of a Deblur or DADA2 run.
tree : Phylogeny[Rooted]
    The tree resulting from inserting fragments into a reference phylogeny,
    i.e. the output of function 'sepp'

Returns
-------
filtered_table : FeatureTable[Frequency]
    The input table minus those fragments that were not part of the tree.
    This feature-table can be used for downstream analyses like
    phylogenetic alpha- or beta- diversity computation.
removed_table : FeatureTable[Frequency]
    Those fragments that got removed from the input table, because they
    were not part of the tree. This table is mainly used for quality
    control, e.g. to inspect the ratio of removed reads per sample from the
    input table. You can ignore this table for downstream analyses.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>