annotate qiime2/qiime_feature-table_presence-absence.xml @ 9:f190567fe3f6 draft

Uploaded
author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents 370e0b6e9826
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_feature-table_presence-absence" name="qiime feature-table presence-absence" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Convert to presence/absence</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 feature-table presence-absence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-table=$itable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --o-presence-absence-table=opresenceabsencetable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 cp opresenceabsencetable.qza $opresenceabsencetable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table to be converted into presence/absence abundances. [required]" name="itable" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 <data format="qza" label="${tool.name} on ${on_string}: presenceabsencetable.qza" name="opresenceabsencetable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 Convert to presence/absence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 ###########################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 Convert frequencies to binary values indicating presence or absence of a
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 feature in a sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 table : FeatureTable[Frequency | RelativeFrequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 The feature table to be converted into presence/absence abundances.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 presence_absence_table : FeatureTable[PresenceAbsence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 The resulting presence/absence feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 </tool>