Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_fragment-insertion_filter-features.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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28:c28331a63dfd | 29:3ba9833030c1 |
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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> |