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comparison qiime2/qiime_diversity_alpha-group-significance.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_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.7"> 2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance"
3 <description> - Alpha diversity comparisons</description> 3 version="2020.8">
4 <requirements> 4 <description>Alpha diversity comparisons</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 diversity alpha-group-significance 9 qiime diversity alpha-group-significance
9 10
10 --i-alpha-diversity=$ialphadiversity 11 --i-alpha-diversity=$ialphadiversity
12 # if $input_files_mmetadatafile:
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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
11 22
23 --o-visualization=ovisualization
12 24
13 #if $input_files_mmetadatafile: 25 #if str($examples) != 'None':
14 #def list_dict_to_string(list_dict): 26 --examples=$examples
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
22 #end if 27 #end if
23 28
29 ;
30 cp oalphadiversity.qza $oalphadiversity
24 31
25 --o-visualization=ovisualization
26 ; 32 ;
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 33 qiime tools export ovisualization.qzv --output-path out
34 && mkdir -p '$ovisualization.files_path'
28 && cp -r out/* '$ovisualization.files_path' 35 && cp -r out/* '$ovisualization.files_path'
29 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
30 ]]></command>
31 <inputs>
32 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
33 37
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 38 ;
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 39 qiime tools export ovisualization.qzv --output-path out
36 </repeat> 40 && mkdir -p '$ovisualization.files_path'
37 </inputs> 41 && cp -r out/* '$ovisualization.files_path'
38 <outputs> 42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 43
40 </outputs> 44 ]]></command>
41 <help><![CDATA[ 45 <inputs>
46 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" />
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
48 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
49 </repeat>
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
51
52 </inputs>
53
54 <outputs>
55 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
56
57 </outputs>
58
59 <help><![CDATA[
42 Alpha diversity comparisons 60 Alpha diversity comparisons
61 ###############################################################
43 62
44 Visually and statistically compare groups of alpha diversity values. 63 Visually and statistically compare groups of alpha diversity values.
45 64
46 Parameters 65 Parameters
47 ---------- 66 ----------
51 The sample metadata. 70 The sample metadata.
52 71
53 Returns 72 Returns
54 ------- 73 -------
55 visualization : Visualization 74 visualization : Visualization
56 ]]></help> 75 ]]></help>
57 <macros> 76 <macros>
58 <import>qiime_citation.xml</import> 77 <import>qiime_citation.xml</import>
59 </macros> 78 </macros>
60 <expand macro="qiime_citation"/> 79 <expand macro="qiime_citation"/>
61 </tool> 80 </tool>