Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_feature-table_tabulate-seqs.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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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> |