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comparison qiime2-2020.8/qiime_diversity_alpha-rarefaction.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction"
3 version="2020.8">
4 <description>Alpha rarefaction curves</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity alpha-rarefaction
10
11 --i-table=$itable
12
13 #if str($iphylogeny) != 'None':
14 --i-phylogeny=$iphylogeny
15 #end if
16
17 --p-max-depth=$pmaxdepth
18
19 #if str($pmetrics) != 'None':
20 --p-metrics=$pmetrics
21 #end if
22 # if $input_files_mmetadatafile:
23 # def list_dict_to_string(list_dict):
24 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
25 # for d in list_dict[1:]:
26 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
27 # end for
28 # return $file_list
29 # end def
30 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
31 # end if
32
33 --p-min-depth=$pmindepth
34
35 --p-steps=$psteps
36
37 --p-iterations=$piterations
38
39 --o-visualization=ovisualization
40
41 #if str($examples) != 'None':
42 --examples=$examples
43 #end if
44
45 ;
46 cp oalphadiversity.qza $oalphadiversity
47
48 ;
49 qiime tools export ovisualization.qzv --output-path out
50 && mkdir -p '$ovisualization.files_path'
51 && cp -r out/* '$ovisualization.files_path'
52 && mv '$ovisualization.files_path/index.html' '$ovisualization'
53
54 ]]></command>
55 <inputs>
56 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data" />
57 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted] [optional]" name="iphylogeny" optional="False" type="data" />
58 <param label="--p-max-depth: INTEGER The maximum rarefaction depth. Must be greater than Range(1, None) min-depth. [required]" name="pmaxdepth" optional="False" type="text" />
59 <param label="--p-metrics: " multiple="True" name="pmetrics" optional="True" type="select">
60 <option selected="True" value="None">Selection is Optional</option>
61 <option value="observed_features">observed_features</option>
62 <option value="heip_e">heip_e</option>
63 <option value="dominance">dominance</option>
64 <option value="goods_coverage">goods_coverage</option>
65 <option value="ace">ace</option>
66 <option value="gini_index">gini_index</option>
67 <option value="simpson_e">simpson_e</option>
68 <option value="pielou_e">pielou_e</option>
69 <option value="mcintosh_e">mcintosh_e</option>
70 <option value="berger_parker_d">berger_parker_d</option>
71 <option value="shannon">shannon</option>
72 <option value="enspie">enspie</option>
73 <option value="mcintosh_d">mcintosh_d</option>
74 <option value="lladser_pe">lladser_pe</option>
75 <option value="brillouin_d">brillouin_d</option>
76 <option value="menhinick">menhinick</option>
77 <option value="simpson">simpson</option>
78 <option value="margalef">margalef</option>
79 <option value="robbins">robbins</option>
80 <option value="doubles">doubles</option>
81 <option value="chao1">chao1</option>
82 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
83 <option value="singles">singles</option>
84 <option value="faith_pd">faith_pd</option>
85 <option value="fisher_alpha">fisher_alpha</option>
86 </param>
87 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
88 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata. will be merged) [optional]" name="additional_input" optional="True" type="data" />
89 </repeat>
90 <param label="--p-min-depth: INTEGER The minimum rarefaction depth. Range(1, None) [default: 1]" min="1" name="pmindepth" optional="True" type="integer" value="1" />
91 <param label="--p-steps: INTEGER The number of rarefaction depths to include between Range(2, None) min-depth and max-depth. [default: 10]" min="2" name="psteps" optional="True" type="integer" value="10" />
92 <param label="--p-iterations: INTEGER The number of rarefied feature tables to compute at Range(1, None) each step. [default: 10]" min="1" name="piterations" optional="True" type="integer" value="10" />
93 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
94
95 </inputs>
96
97 <outputs>
98 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
99
100 </outputs>
101
102 <help><![CDATA[
103 Alpha rarefaction curves
104 ###############################################################
105
106 Generate interactive alpha rarefaction curves by computing rarefactions
107 between `min_depth` and `max_depth`. The number of intermediate depths to
108 compute is controlled by the `steps` parameter, with n `iterations` being
109 computed at each rarefaction depth. If sample metadata is provided, samples
110 may be grouped based on distinct values within a metadata column.
111
112 Parameters
113 ----------
114 table : FeatureTable[Frequency]
115 Feature table to compute rarefaction curves from.
116 max_depth : Int % Range(1, None)
117 The maximum rarefaction depth. Must be greater than min_depth.
118 phylogeny : Phylogeny[Rooted], optional
119 Optional phylogeny for phylogenetic metrics.
120 metrics : Set[Str % Choices('mcintosh_e', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'faith_pd', 'menhinick', 'pielou_e', 'shannon', 'singles', 'simpson', 'fisher_alpha', 'dominance', 'robbins', 'lladser_pe', 'mcintosh_d', 'brillouin_d', 'goods_coverage')], optional
121 The metrics to be measured. By default computes observed_features,
122 shannon, and if phylogeny is provided, faith_pd.
123 metadata : Metadata, optional
124 The sample metadata.
125 min_depth : Int % Range(1, None), optional
126 The minimum rarefaction depth.
127 steps : Int % Range(2, None), optional
128 The number of rarefaction depths to include between min_depth and
129 max_depth.
130 iterations : Int % Range(1, None), optional
131 The number of rarefied feature tables to compute at each step.
132
133 Returns
134 -------
135 visualization : Visualization
136 ]]></help>
137 <macros>
138 <import>qiime_citation.xml</import>
139 </macros>
140 <expand macro="qiime_citation"/>
141 </tool>