annotate qiime2/qiime_demux_subsample-single.xml @ 0:370e0b6e9826 draft

Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children f190567fe3f6
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" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_demux_subsample-single" name="qiime demux subsample-single" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Subsample single-end sequences without replacement.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
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 demux subsample-single
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-sequences=$isequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --p-fraction="$pfraction"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --o-subsampled-sequences=osubsampledsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 cp osubsampledsequences.qza $osubsampledsequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The demultiplexed sequences to be subsampled. [required]" name="isequences" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 <param label="--p-fraction: PROPORTION Range(0, 1, inclusive_start=False) The fraction of sequences to retain in subsample. [required]" name="pfraction" optional="False" exclude_min="True" min="0" max="1" value="" type="float"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <data format="qza" label="${tool.name} on ${on_string}: subsampledsequences.qza" name="osubsampledsequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 Subsample single-end sequences without replacement.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 ###################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 Generate a random subsample of single-end sequences containing
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 approximately the fraction of input sequences specified by the fraction
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 parameter. The number of output samples will always be equal to the number
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 of input samples, even if some of those samples contain no sequences after
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 subsampling.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 sequences : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 The demultiplexed sequences to be subsampled.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 fraction : Float % Range(0, 1, inclusive_start=False)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 The fraction of sequences to retain in subsample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 subsampled_sequences : SampleData[SequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 The subsampled sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 </tool>