annotate qiime2/qiime_diversity_alpha-phylogenetic.xml @ 11:ea7a1c6be3c4 draft

Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:37:40 +0000
parents f190567fe3f6
children a0a8d77a991c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 0
diff changeset
2 <tool id="qiime_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Alpha diversity (phylogenetic)</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 0
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime diversity alpha-phylogenetic
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-phylogeny=$iphylogeny
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-metric=$pmetric
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 --o-alpha-diversity=oalphadiversity
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 cp oalphadiversity.qza $oalphadiversity
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <param label="--p-metric: " name="pmetric" optional="False" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <option value="faith_pd">faith_pd</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 Alpha diversity (phylogenetic)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 ##############################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 Computes a user-specified phylogenetic alpha diversity metric for all
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 samples in a feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 The feature table containing the samples for which alpha diversity
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 should be computed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 phylogeny : Phylogeny[Rooted]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 Phylogenetic tree containing tip identifiers that correspond to the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 feature identifiers in the table. This tree can contain tip ids that
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 are not present in the table, but all feature ids in the table must be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 present in this tree.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 metric : Str % Choices('faith_pd')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 The alpha diversity metric to be computed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 Vector containing per-sample alpha diversities.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 </tool>