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comparison qiime2/qiime_feature-table_tabulate-seqs.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.7"> 2 <tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs"
3 <description> - View sequence associated with each feature</description> 3 version="2020.8">
4 <requirements> 4 <description>View sequence associated with each feature</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime feature-table tabulate-seqs 9 qiime feature-table tabulate-seqs
9 10 # if $input_files_idata:
10 --i-data=$idata 11 # def list_dict_to_string(list_dict):
12 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 # for d in list_dict[1:]:
14 # set $file_list = $file_list + ' --i-data=' + d['additional_input'].__getattr__('file_name')
15 # end for
16 # return $file_list
17 # end def
18 --i-data=$list_dict_to_string($input_files_idata)
19 # end if
11 20
12 --o-visualization=ovisualization 21 --o-visualization=ovisualization
22
23 #if str($examples) != 'None':
24 --examples=$examples
25 #end if
26
13 ; 27 ;
14 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 28 cp osampledtable.qza $osampledtable
29
30 ;
31 qiime tools export ovisualization.qzv --output-path out
32 && mkdir -p '$ovisualization.files_path'
15 && cp -r out/* '$ovisualization.files_path' 33 && cp -r out/* '$ovisualization.files_path'
16 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
17 ]]></command> 35
18 <inputs> 36 ;
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"/> 37 qiime tools export ovisualization.qzv --output-path out
20 </inputs> 38 && mkdir -p '$ovisualization.files_path'
21 <outputs> 39 && cp -r out/* '$ovisualization.files_path'
22 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 40 && mv '$ovisualization.files_path/index.html' '$ovisualization'
23 </outputs> 41
24 <help><![CDATA[ 42 ]]></command>
43 <inputs>
44 <repeat name="input_files_idata" optional="False" title="--i-data">
45 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required]" name="additional_input" optional="False" type="data" />
46 </repeat>
47 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
48
49 </inputs>
50
51 <outputs>
52 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
53
54 </outputs>
55
56 <help><![CDATA[
25 View sequence associated with each feature 57 View sequence associated with each feature
26 ########################################## 58 ###############################################################
27 59
28 Generate tabular view of feature identifier to sequence mapping, including 60 Generate tabular view of feature identifier to sequence mapping, including
29 links to BLAST each sequence against the NCBI nt database. 61 links to BLAST each sequence against the NCBI nt database.
30 62
31 Parameters 63 Parameters
32 ---------- 64 ----------
33 data : FeatureData[Sequence] 65 data : FeatureData[Sequence | AlignedSequence]
34 The feature sequences to be tabulated. 66 The feature sequences to be tabulated.
35 67
36 Returns 68 Returns
37 ------- 69 -------
38 visualization : Visualization 70 visualization : Visualization
39 ]]></help> 71 ]]></help>
40 <macros> 72 <macros>
41 <import>qiime_citation.xml</import> 73 <import>qiime_citation.xml</import>
42 </macros> 74 </macros>
43 <expand macro="qiime_citation"/> 75 <expand macro="qiime_citation"/>
44 </tool> 76 </tool>