Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_fragment-insertion_filter-features.xml @ 0:370e0b6e9826 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children f190567fe3f6
comparison
equal deleted inserted replaced
-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features" version="2019.4">
3 <description> - Filter fragments in tree from table.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime fragment-insertion filter-features
9
10 --i-table=$itable
11 --i-tree=$itree
12
13 --o-filtered-table=ofilteredtable
14 --o-removed-table=oremovedtable
15 ;
16 cp ofilteredtable.qza $ofilteredtable;
17 cp oremovedtable.qza $oremovedtable
18 ]]></command>
19 <inputs>
20 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]" name="itable" optional="False" type="data"/>
21 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/>
22 </inputs>
23 <outputs>
24 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
25 <data format="qza" label="${tool.name} on ${on_string}: removedtable.qza" name="oremovedtable"/>
26 </outputs>
27 <help><![CDATA[
28 Filter fragments in tree from table.
29 ####################################
30
31 Filters fragments not inserted into a phylogenetic tree from a feature-
32 table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
33 get inserted by SEPP into a reference phylogeny. To be able to use the
34 feature-table for downstream analyses like computing Faith's PD or UniFrac,
35 the feature-table must be cleared of fragments that are not part of the
36 phylogenetic tree, because their path length can otherwise not be
37 determined. Typically, the number of rejected fragments is low (<= 10), but
38 it might be worth to inspect the ratio of reads assigned to those rejected
39 fragments.
40
41 Parameters
42 ----------
43 table : FeatureTable[Frequency]
44 A feature-table which needs to filtered down to those fragments that
45 are contained in the tree, e.g. result of a Deblur or DADA2 run.
46 tree : Phylogeny[Rooted]
47 The tree resulting from inserting fragments into a reference phylogeny,
48 i.e. the output of function 'sepp'
49
50 Returns
51 -------
52 filtered_table : FeatureTable[Frequency]
53 The input table minus those fragments that were not part of the tree.
54 This feature-table can be used for downstream analyses like
55 phylogenetic alpha- or beta- diversity computation.
56 removed_table : FeatureTable[Frequency]
57 Those fragments that got removed from the input table, because they
58 were not part of the tree. This table is mainly used for quality
59 control, e.g. to inspect the ratio of removed reads per sample from the
60 input table. You can ignore this table for downstream analyses.
61 ]]></help>
62 <macros>
63 <import>qiime_citation.xml</import>
64 </macros>
65 <expand macro="qiime_citation"/>
66 </tool>