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comparison qiime2-2020.8/qiime_fragment-insertion_filter-features.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features"
3 version="2020.8">
4 <description>Filter fragments in tree from table.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime fragment-insertion filter-features
10
11 --i-table=$itable
12
13 --i-tree=$itree
14
15 --o-filtered-table=ofilteredtable
16
17 --o-removed-table=oremovedtable
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp oremovedtable.qza $oremovedtable
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]" name="itable" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
31
32 </inputs>
33
34 <outputs>
35 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
36 <data format="qza" label="${tool.name} on ${on_string}: removedtable.qza" name="oremovedtable" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Filter fragments in tree from table.
42 ###############################################################
43
44 Filters fragments not inserted into a phylogenetic tree from a feature-
45 table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
46 get inserted by SEPP into a reference phylogeny. To be able to use the
47 feature-table for downstream analyses like computing Faith's PD or UniFrac,
48 the feature-table must be cleared of fragments that are not part of the
49 phylogenetic tree, because their path length can otherwise not be
50 determined. Typically, the number of rejected fragments is low (<= 10), but
51 it might be worth to inspect the ratio of reads assigned to those rejected
52 fragments.
53
54 Parameters
55 ----------
56 table : FeatureTable[Frequency]
57 A feature-table which needs to filtered down to those fragments that
58 are contained in the tree, e.g. result of a Deblur or DADA2 run.
59 tree : Phylogeny[Rooted]
60 The tree resulting from inserting fragments into a reference phylogeny,
61 i.e. the output of function 'sepp'
62
63 Returns
64 -------
65 filtered_table : FeatureTable[Frequency]
66 The input table minus those fragments that were not part of the tree.
67 This feature-table can be used for downstream analyses like
68 phylogenetic alpha- or beta- diversity computation.
69 removed_table : FeatureTable[Frequency]
70 Those fragments that got removed from the input table, because they
71 were not part of the tree. This table is mainly used for quality
72 control, e.g. to inspect the ratio of removed reads per sample from the
73 input table. You can ignore this table for downstream analyses.
74 ]]></help>
75 <macros>
76 <import>qiime_citation.xml</import>
77 </macros>
78 <expand macro="qiime_citation"/>
79 </tool>