|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.4">
|
|
|
3 <description> - Alpha rarefaction curves</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity alpha-rarefaction
|
|
|
9
|
|
|
10 --i-table=$itable
|
|
|
11 --p-max-depth="$pmaxdepth"
|
|
|
12
|
|
|
13 #if str($iphylogeny) != 'None':
|
|
|
14 --i-phylogeny=$iphylogeny
|
|
|
15 #end if
|
|
|
16
|
|
|
17 #if str($pmetrics) != 'None':
|
|
|
18 --p-metrics=$pmetrics
|
|
|
19 #end if
|
|
|
20
|
|
|
21
|
|
|
22 #if $pmindepth:
|
|
|
23 --p-min-depth=$pmindepth
|
|
|
24 #end if
|
|
|
25
|
|
|
26 #if $psteps:
|
|
|
27 --p-steps=$psteps
|
|
|
28 #end if
|
|
|
29
|
|
|
30 #if $piterations:
|
|
|
31 --p-iterations=$piterations
|
|
|
32 #end if
|
|
|
33
|
|
|
34 #if $input_files_mmetadatafile:
|
|
|
35 #def list_dict_to_string(list_dict):
|
|
|
36 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
37 #for d in list_dict[1:]:
|
|
|
38 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
|
39 #end for
|
|
|
40 #return $file_list
|
|
|
41 #end def
|
|
|
42 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
43 #end if
|
|
|
44
|
|
|
45 --o-visualization=ovisualization
|
|
|
46 ;
|
|
|
47 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
48 && cp -r out/* '$ovisualization.files_path'
|
|
|
49 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
50 ]]></command>
|
|
|
51 <inputs>
|
|
|
52 <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"/>
|
|
|
53 <param label="--p-max-depth: INTEGER The maximum rarefaction depth. Must be greater than Range(1, None) min-depth. [required]" name="pmaxdepth" optional="False" min="1" value="" type="integer"/>
|
|
|
54 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted] [optional]" name="iphylogeny" optional="True" type="data"/>
|
|
|
55 <param label="--p-metrics: " name="pmetrics" optional="True" type="select">
|
|
|
56 <option selected="True" value="None">Selection is Optional</option>
|
|
|
57 <option value="dominance">dominance</option>
|
|
|
58 <option value="ace">ace</option>
|
|
|
59 <option value="brillouin_d">brillouin_d</option>
|
|
|
60 <option value="margalef">margalef</option>
|
|
|
61 <option value="menhinick">menhinick</option>
|
|
|
62 <option value="mcintosh_d">mcintosh_d</option>
|
|
|
63 <option value="berger_parker_d">berger_parker_d</option>
|
|
|
64 <option value="enspie">enspie</option>
|
|
|
65 <option value="doubles">doubles</option>
|
|
|
66 <option value="lladser_pe">lladser_pe</option>
|
|
|
67 <option value="observed_otus">observed_otus</option>
|
|
|
68 <option value="faith_pd">faith_pd</option>
|
|
|
69 <option value="simpson_e">simpson_e</option>
|
|
|
70 <option value="robbins">robbins</option>
|
|
|
71 <option value="shannon">shannon</option>
|
|
|
72 <option value="pielou_e">pielou_e</option>
|
|
|
73 <option value="singles">singles</option>
|
|
|
74 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
|
|
|
75 <option value="heip_e">heip_e</option>
|
|
|
76 <option value="mcintosh_e">mcintosh_e</option>
|
|
|
77 <option value="fisher_alpha">fisher_alpha</option>
|
|
|
78 <option value="goods_coverage">goods_coverage</option>
|
|
|
79 <option value="chao1">chao1</option>
|
|
|
80 <option value="gini_index">gini_index</option>
|
|
|
81 <option value="simpson">simpson</option>
|
|
|
82 </param>
|
|
|
83 <param label="--p-min-depth: INTEGER The minimum rarefaction depth. Range(1, None) [default: 1]" name="pmindepth" optional="True" type="integer" min="1" value="1"/>
|
|
|
84 <param label="--p-steps: INTEGER The number of rarefaction depths to include between Range(2, None) min-depth and max-depth. [default: 10]" name="psteps" optional="True" type="integer" min="2" value="10"/>
|
|
|
85 <param label="--p-iterations: INTEGER The number of rarefied feature tables to compute at Range(1, None) each step. [default: 10]" name="piterations" optional="True" type="integer" min="1" value="10"/>
|
|
|
86
|
|
|
87 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
|
88 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
89 </repeat>
|
|
|
90
|
|
|
91 </inputs>
|
|
|
92 <outputs>
|
|
|
93 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
94 </outputs>
|
|
|
95 <help><![CDATA[
|
|
|
96 Alpha rarefaction curves
|
|
|
97 ########################
|
|
|
98
|
|
|
99 Generate interactive alpha rarefaction curves by computing rarefactions
|
|
|
100 between `min_depth` and `max_depth`. The number of intermediate depths to
|
|
|
101 compute is controlled by the `steps` parameter, with n `iterations` being
|
|
|
102 computed at each rarefaction depth. If sample metadata is provided, samples
|
|
|
103 may be grouped based on distinct values within a metadata column.
|
|
|
104
|
|
|
105 Parameters
|
|
|
106 ----------
|
|
|
107 table : FeatureTable[Frequency]
|
|
|
108 Feature table to compute rarefaction curves from.
|
|
|
109 max_depth : Int % Range(1, None)
|
|
|
110 The maximum rarefaction depth. Must be greater than min_depth.
|
|
|
111 phylogeny : Phylogeny[Rooted], optional
|
|
|
112 Optional phylogeny for phylogenetic metrics.
|
|
|
113 metrics : Set[Str % Choices('pielou_e', 'simpson_e', 'shannon', 'margalef', 'menhinick', 'brillouin_d', 'mcintosh_e', 'doubles', 'robbins', 'simpson', 'enspie', 'fisher_alpha', 'heip_e', 'singles', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'goods_coverage', 'mcintosh_d', 'faith_pd', 'ace', 'chao1', 'lladser_pe', 'berger_parker_d')], optional
|
|
|
114 The metrics to be measured. By default computes observed_otus, shannon,
|
|
|
115 and if phylogeny is provided, faith_pd.
|
|
|
116 metadata : Metadata, optional
|
|
|
117 The sample metadata.
|
|
|
118 min_depth : Int % Range(1, None), optional
|
|
|
119 The minimum rarefaction depth.
|
|
|
120 steps : Int % Range(2, None), optional
|
|
|
121 The number of rarefaction depths to include between min_depth and
|
|
|
122 max_depth.
|
|
|
123 iterations : Int % Range(1, None), optional
|
|
|
124 The number of rarefied feature tables to compute at each step.
|
|
|
125
|
|
|
126 Returns
|
|
|
127 -------
|
|
|
128 visualization : Visualization
|
|
|
129 ]]></help>
|
|
|
130 <macros>
|
|
|
131 <import>qiime_citation.xml</import>
|
|
|
132 </macros>
|
|
|
133 <expand macro="qiime_citation"/>
|
|
|
134 </tool>
|
