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comparison qiime2/qiime_taxa_barplot.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_taxa_barplot" name="qiime taxa barplot" version="2019.7"> 2 <tool id="qiime_taxa_barplot" name="qiime taxa barplot"
3 <description> - Visualize taxonomy with an interactive bar plot</description> 3 version="2020.8">
4 <requirements> 4 <description>Visualize taxonomy with an interactive bar plot</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 taxa barplot 9 qiime taxa barplot
9
10
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
13 --i-taxonomy '$tax'
14 #else:
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
16 --i-taxonomy '$tax'
17 #end if
18
19 10
20 --i-table=$itable 11 --i-table=$itable
21 12
22 #if $input_files_mmetadatafile: 13 --i-taxonomy=$itaxonomy
23 #def list_dict_to_string(list_dict): 14 # if $input_files_mmetadatafile:
24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 15 # def list_dict_to_string(list_dict):
25 #for d in list_dict[1:]: 16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
26 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') 17 # for d in list_dict[1:]:
27 #end for 18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
28 #return $file_list 19 # end for
29 #end def 20 # return $file_list
30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) 21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 --o-visualization=ovisualization
26
27 #if str($examples) != 'None':
28 --examples=$examples
31 #end if 29 #end if
32 30
33 --o-visualization=ovisualization
34 ; 31 ;
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 32 cp otesttable.qza $otesttable
33
34 ;
35 qiime tools export ovisualization.qzv --output-path out
36 && mkdir -p '$ovisualization.files_path'
36 && cp -r out/* '$ovisualization.files_path' 37 && cp -r out/* '$ovisualization.files_path'
37 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
38 ]]></command>
39 <inputs>
40 39
41 <conditional name="id_to_taxonomy_fp" optional="True"> 40 ;
42 <param name="selector" type="select" label="Reference taxonomy to query"> 41 qiime tools export ovisualization.qzv --output-path out
43 <option value="cached">Public databases</option> 42 && mkdir -p '$ovisualization.files_path'
44 <option value="history">Databases from your history</option> 43 && cp -r out/* '$ovisualization.files_path'
45 </param> 44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
46 <when value="cached">
47 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
48 <options from_data_table="qiime_taxonomy" />
49 </param>
50 </when>
51 <when value="history">
52 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
53 </when>
54 </conditional>
55 45
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data" />
49 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
50 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
51 <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" />
52 </repeat>
53 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
54
55 </inputs>
56 56
57 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels. [required]" name="itable" optional="False" type="data"/> 57 <outputs>
58 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
59
60 </outputs>
58 61
59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]"> 62 <help><![CDATA[
60 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" optional="False" />
61 </repeat>
62
63 </inputs>
64 <outputs>
65 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
66 </outputs>
67 <help><![CDATA[
68 Visualize taxonomy with an interactive bar plot 63 Visualize taxonomy with an interactive bar plot
69 ############################################### 64 ###############################################################
70 65
71 This visualizer produces an interactive barplot visualization of 66 This visualizer produces an interactive barplot visualization of
72 taxonomies. Interactive features include multi-level sorting, plot 67 taxonomies. Interactive features include multi-level sorting, plot
73 recoloring, sample relabeling, and SVG figure export. 68 recoloring, sample relabeling, and SVG figure export.
74 69
85 The sample metadata. 80 The sample metadata.
86 81
87 Returns 82 Returns
88 ------- 83 -------
89 visualization : Visualization 84 visualization : Visualization
90 ]]></help> 85 ]]></help>
91 <macros> 86 <macros>
92 <import>qiime_citation.xml</import> 87 <import>qiime_citation.xml</import>
93 </macros> 88 </macros>
94 <expand macro="qiime_citation"/> 89 <expand macro="qiime_citation"/>
95 </tool> 90 </tool>