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comparison qiime2/qiime_feature-table_summarize.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_summarize" name="qiime feature-table summarize" version="2019.7"> 2 <tool id="qiime_feature-table_summarize" name="qiime feature-table summarize"
3 <description> - Summarize table</description> 3 version="2020.8">
4 <requirements> 4 <description>Summarize table</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 summarize 9 qiime feature-table summarize
9 10
10 --i-table=$itable 11 --i-table=$itable
12 # if $input_files_msamplemetadatafile:
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-sample-metadata-file=' + 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
11 22
23 --o-visualization=ovisualization
12 24
13 #if $m_sample_metadatafile: 25 #if str($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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
22 #end if 27 #end if
23 28
29 ;
30 cp osampledtable.qza $osampledtable
24 31
25 --o-visualization=ovisualization
26 ; 32 ;
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$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' '$ovisualization'
30 ]]></command>
31 <inputs>
32 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
33 37
34 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file"> 38 ]]></command>
35 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 39 <inputs>
36 </repeat> 40 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data" />
37 </inputs> 41 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
38 <outputs> 42 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [optional]" name="additional_input" optional="True" type="data" />
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 43 </repeat>
40 </outputs> 44 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
41 <help><![CDATA[ 45
46 </inputs>
47
48 <outputs>
49 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
50
51 </outputs>
52
53 <help><![CDATA[
42 Summarize table 54 Summarize table
43 ############### 55 ###############################################################
44 56
45 Generate visual and tabular summaries of a feature table. 57 Generate visual and tabular summaries of a feature table.
46 58
47 Parameters 59 Parameters
48 ---------- 60 ----------
52 The sample metadata. 64 The sample metadata.
53 65
54 Returns 66 Returns
55 ------- 67 -------
56 visualization : Visualization 68 visualization : Visualization
57 ]]></help> 69 ]]></help>
58 <macros> 70 <macros>
59 <import>qiime_citation.xml</import> 71 <import>qiime_citation.xml</import>
60 </macros> 72 </macros>
61 <expand macro="qiime_citation"/> 73 <expand macro="qiime_citation"/>
62 </tool> 74 </tool>