Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_feature-table_summarize.xml @ 0:51b9b6b57732 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:51b9b6b57732
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2018.4">
3 <description> - Summarize table</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime feature-table summarize --i-table=$itable
10
11 #if $input_files_msamplemetadatafile:
12
13 #def list_dict_to_string(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
17 #end for
18 #return $file_list
19 #end def
20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
21 #end if
22
23 #if str($cmdconfig) != 'None':
24 --cmd-config=$cmdconfig
25 #end if
26 --o-visualization=ovisualization;
27
28 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
29 && cp -r out/* '$ovisualization.files_path'
30 && mv '$ovisualization.files_path/index.html' '$ovisualization'
31 ]]>
32 </command>
33 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency | PresenceAbsence | RelativeFrequency] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
35 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
36 <param label="--m-sample-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
37 </repeat>
38 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
39 </inputs>
40 <outputs>
41 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
42 </outputs>
43 <help>
44 <![CDATA[
45 Summarize table
46 ----------------
47
48 Generate visual and tabular summaries of a feature table.
49
50 Parameters
51 ----------
52 table : FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]
53 The feature table to be summarized.
54 sample_metadata : Metadata, optional
55 The sample metadata.
56
57 Returns
58 -------
59 visualization : Visualization
60 \
61 ]]>
62 </help>
63 <macros>
64 <import>qiime_citation.xml</import>
65 </macros>
66 <expand macro="qiime_citation" />
67 </tool>