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comparison qiime2/qiime_diversity_alpha-rarefaction.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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>