Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_taxa_barplot.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime taxa barplot 8 qiime taxa barplot
9 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 --i-table=$itable 20 --i-table=$itable
11 --i-taxonomy=$itaxonomy
12 21
13 #if $input_files_mmetadatafile: 22 #if $input_files_mmetadatafile:
14 #def list_dict_to_string(list_dict): 23 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 24 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]: 25 #for d in list_dict[1:]:
26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
27 && cp -r out/* '$ovisualization.files_path' 36 && cp -r out/* '$ovisualization.files_path'
28 && mv '$ovisualization.files_path/index.html' '$ovisualization'; 37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
29 ]]></command> 38 ]]></command>
30 <inputs> 39 <inputs>
40
41 <conditional name="id_to_taxonomy_fp" optional="True">
42 <param name="selector" type="select" label="Reference taxonomy to query">
43 <option value="cached">Public databases</option>
44 <option value="history">Databases from your history</option>
45 </param>
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
56
31 <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 <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"/>
32 <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"/>
33 58
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]"> 59 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file [required]">
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" /> 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" />
36 </repeat> 61 </repeat>
37 62
38 </inputs> 63 </inputs>
39 <outputs> 64 <outputs>
40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 65 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>