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comparison qiime2/qiime_diversity_alpha-rarefaction.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2018.4">
3 <description> - Alpha rarefaction curves</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity alpha-rarefaction --p-max-depth="$pmaxdepth" --i-table=$itable
9
10 #if str($pmetrics) != 'None':
11 --p-metrics=$pmetrics
12 #end if
13
14 #if $pmindepth:
15 --p-min-depth=$pmindepth
16 #end if
17
18 #if $piterations:
19 --p-iterations=$piterations
20 #end if
21
22 #if str($cmdconfig) != 'None':
23 --cmd-config=$cmdconfig
24 #end if
25
26 #if $input_files_mmetadatafile:
27
28 #def list_dict_to_string(list_dict):
29 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
30 #for d in list_dict[1:]:
31 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
32 #end for
33 #return $file_list
34 #end def
35 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
36 #end if
37
38 #if $psteps:
39 --p-steps=$psteps
40 #end if
41
42 #if str($iphylogeny) != 'None':
43 --i-phylogeny=$iphylogeny
44 #end if
45
46 --o-visualization=ovisualization;
47 qiime tools export ovisualization.qzv --output-dir 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: FeatureTable[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data"/>
53 <param label="--p-max-depth: The maximum rarefaction depth. Must be greater than min_depth. [required]" name="pmaxdepth" optional="False" type="text"/>
54 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Optional phylogeny for phylogenetic metrics. [optional]" name="iphylogeny" optional="True" type="data"/>
55 <param name="pmetrics" optional="True" type="select" label="--p-metrics: The metrics to be measured. By default
56 computes observed_otus, shannon, and if
57 phylogeny is provided, faith_pd. [optional]">
58 <option selected="True" value="None">Selection is Optional</option>
59 <option value="goods_coverage">goods_coverage</option>
60 <option value="heip_e">heip_e</option>
61 <option value="mcintosh_d">mcintosh_d</option>
62 <option value="observed_otus">observed_otus</option>
63 <option value="doubles">doubles</option>
64 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
65 <option value="shannon">shannon</option>
66 <option value="margalef">margalef</option>
67 <option value="simpson">simpson</option>
68 <option value="lladser_pe">lladser_pe</option>
69 <option value="menhinick">menhinick</option>
70 <option value="singles">singles</option>
71 <option value="gini_index">gini_index</option>
72 <option value="robbins">robbins</option>
73 <option value="ace">ace</option>
74 <option value="simpson_e">simpson_e</option>
75 <option value="enspie">enspie</option>
76 <option value="berger_parker_d">berger_parker_d</option>
77 <option value="fisher_alpha">fisher_alpha</option>
78 <option value="dominance">dominance</option>
79 <option value="pielou_e">pielou_e</option>
80 <option value="chao1">chao1</option>
81 <option value="mcintosh_e">mcintosh_e</option>
82 <option value="faith_pd">faith_pd</option>
83 <option value="brillouin_d">brillouin_d</option>
84 </param>
85 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
86 <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" />
87 </repeat>
88 <param label="--p-min-depth: The minimum rarefaction depth. [default: 1]" name="pmindepth" optional="True" type="integer" value="1"/>
89 <param label="--p-steps: The number of rarefaction depths to include between min_depth and max_depth. [default: 10]" name="psteps" optional="True" type="integer" value="10"/>
90 <param label="--p-iterations: The number of rarefied feature tables to compute at each step. [default: 10]" name="piterations" optional="True" type="integer" value="10"/>
91 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
92 </inputs>
93 <outputs>
94 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
95 </outputs>
96 <help><![CDATA[
97 Alpha rarefaction curves
98 -------------------------
99
100 Generate interactive alpha rarefaction curves by computing rarefactions
101 between \`min_depth\` and \`max_depth\`. The number of intermediate depths to
102 compute is controlled by the \`steps\` parameter, with n \`iterations\` being
103 computed at each rarefaction depth. If sample metadata is provided, samples
104 may be grouped based on distinct values within a metadata column.
105
106 Parameters
107 ----------
108 table : FeatureTable[Frequency]
109 Feature table to compute rarefaction curves from.
110 phylogeny : Phylogeny[Rooted], optional
111 Optional phylogeny for phylogenetic metrics.
112 max_depth : Int % Range(1, None)
113 The maximum rarefaction depth. Must be greater than min_depth.
114 metrics : Set[Str % Choices({'ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'dominance', 'doubles', 'enspie', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_otus', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles'})], optional
115 The metrics to be measured. By default computes observed_otus, shannon,
116 and if phylogeny is provided, faith_pd.
117 metadata : Metadata, optional
118 The sample metadata.
119 min_depth : Int % Range(1, None), optional
120 The minimum rarefaction depth.
121 steps : Int % Range(2, None), optional
122 The number of rarefaction depths to include between min_depth and
123 max_depth.
124 iterations : Int % Range(1, None), optional
125 The number of rarefied feature tables to compute at each step.
126
127 Returns
128 -------
129 visualization : Visualization
130 \
131 ]]>
132 </help>
133 <macros>
134 <import>qiime_citation.xml</import>
135 </macros>
136 <expand macro="qiime_citation" />
137 </tool>