annotate qiime2/qiime_feature-table_tabulate-seqs.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_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - View sequence associated with each feature</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 tabulate-seqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-data=$idata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence] The feature sequences to be tabulated. [required]" name="idata" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 View sequence associated with each feature
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 ##########################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 Generate tabular view of feature identifier to sequence mapping, including
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 links to BLAST each sequence against the NCBI nt database.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 data : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 The feature sequences to be tabulated.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 </tool>