annotate qiime2-2020.8/qiime_demux_subsample-paired.xml @ 20:d93d8888f0b0 draft

Uploaded
author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_demux_subsample-paired" name="qiime demux subsample-paired"
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
3 version="2020.8">
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
4 <description>Subsample paired-end sequences without replacement.</description>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
5 <requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
7 </requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
8 <command><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
9 qiime demux subsample-paired
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
10
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
11 --i-sequences=$isequences
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
12
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
13 --p-fraction=$pfraction
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
14
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
15 --o-subsampled-sequences=osubsampledsequences
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
16
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
17 #if str($examples) != 'None':
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
18 --examples=$examples
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
19 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
20
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
21 ;
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
22 cp osubsampledsequences.qza $osubsampledsequences
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
23
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
24 ]]></command>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
25 <inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
26 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed sequences to be subsampled. [required]" name="isequences" optional="False" type="data" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
27 <param label="--p-fraction: PROPORTION Range(0, 1, inclusive_start=False) The fraction of sequences to retain in subsample. [required]" name="pfraction" optional="False" type="text" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
28 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
29
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
30 </inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
31
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
32 <outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
33 <data format="qza" label="${tool.name} on ${on_string}: subsampledsequences.qza" name="osubsampledsequences" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
34
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
35 </outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
36
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
37 <help><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
38 Subsample paired-end sequences without replacement.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
39 ###############################################################
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
40
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
41 Generate a random subsample of paired-end sequences containing
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
42 approximately the fraction of input sequences specified by the fraction
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
43 parameter. The number of output samples will always be equal to the number
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
44 of input samples, even if some of those samples contain no sequences after
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
45 subsampling.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
46
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
47 Parameters
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
48 ----------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
49 sequences : SampleData[PairedEndSequencesWithQuality]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
50 The demultiplexed sequences to be subsampled.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
51 fraction : Float % Range(0, 1, inclusive_start=False)
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
52 The fraction of sequences to retain in subsample.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
53
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
54 Returns
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
55 -------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
56 subsampled_sequences : SampleData[PairedEndSequencesWithQuality]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
57 The subsampled sequences.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
58 ]]></help>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
59 <macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
60 <import>qiime_citation.xml</import>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
61 </macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
62 <expand macro="qiime_citation"/>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
63 </tool>