annotate qiime2/qiime_demux_summarize.xml @ 7:85b520815e85 draft

Uploaded
author florianbegusch
date Tue, 13 Aug 2019 07:53:59 -0400
parents a025a4a89e07
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_summarize" name="qiime demux summarize" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Summarize counts per sample.</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 summarize
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-data=$idata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
5
a025a4a89e07 Uploaded
florianbegusch
parents: 0
diff changeset
12 #if str($pn):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 --p-n=$pn
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 && mv '$ovisualization.files_path/index.html' '$ovisualization'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="idata" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <param label="--p-n: INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences. [default: 10000]" name="pn" optional="True" type="integer" value="10000"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 Summarize counts per sample.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 ############################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 Summarize counts per sample for all samples, and generate interactive
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 positional quality plots based on `n` randomly selected sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 The demultiplexed sequences to be summarized.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 n : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 The number of sequences that should be selected at random for quality
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 score plots. The quality plots will present the average positional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 qualities across all of the sequences selected. If input sequences are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 paired end, plots will be generated for both forward and reverse reads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 for the same `n` sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 </tool>