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comparison qiime2/qiime_sample-classifier_classify-samples-from-dist.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist" version="2019.7"> 2 <tool id="qiime_sample-classifier_classify-samples-from-dist" name="qiime sample-classifier classify-samples-from-dist"
3 <description> - Run k-nearest-neighbors on a labeled distance matrix.</description> 3 version="2020.8">
4 <requirements> 4 <description>Run k-nearest-neighbors on a labeled distance matrix.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime sample-classifier classify-samples-from-dist 9 qiime sample-classifier classify-samples-from-dist
9 10
10 --i-distance-matrix=$idistancematrix 11 --i-distance-matrix=$idistancematrix
11 --m-metadata-column="$mmetadatacolumn" 12 # if $input_files_mmetadatafile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
21 # end if
12 22
13 #if str($pk): 23 #if '__ob__' in str($mmetadatacolumn):
14 --p-k=$pk 24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
25 #set $mmetadatacolumn = $mmetadatacolumn_temp
26 #end if
27 #if '__cb__' in str($mmetadatacolumn):
28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
29 #set $mmetadatacolumn = $mmetadatacolumn_temp
30 #end if
31 #if 'X' in str($mmetadatacolumn):
32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
33 #set $mmetadatacolumn = $mmetadatacolumn_temp
34 #end if
35 #if '__sq__' in str($mmetadatacolumn):
36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
37 #set $mmetadatacolumn = $mmetadatacolumn_temp
38 #end if
39 #if '__db__' in str($mmetadatacolumn):
40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
41 #set $mmetadatacolumn = $mmetadatacolumn_temp
15 #end if 42 #end if
16 43
44 --m-metadata-column=$mmetadatacolumn
45
46
47 --p-k=$pk
48
17 #if str($ppalette) != 'None': 49 #if str($ppalette) != 'None':
18 --p-palette=$ppalette 50 --p-palette=$ppalette
19 #end if 51 #end if
20 52
53 --o-predictions=opredictions
21 54
22 #if $metadatafile: 55 --o-accuracy-results=oaccuracyresults
23 --m-metadata-file=$metadatafile 56
57 #if str($examples) != 'None':
58 --examples=$examples
24 #end if 59 #end if
25 60
61 ;
62 cp opredictions.qza $opredictions
26 63
27 --o-predictions=opredictions
28 --o-accuracy-results=oaccuracyresults
29 ; 64 ;
30 cp opredictions.qza $opredictions; 65 qiime tools export oaccuracyresults.qzv --output-path out
31 qiime tools export --input-path oaccuracyresults.qzv --output-path out && mkdir -p '$oaccuracyresults.files_path' 66 && mkdir -p '$oaccuracyresults.files_path'
32 && cp -r out/* '$oaccuracyresults.files_path' 67 && cp -r out/* '$oaccuracyresults.files_path'
33 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults' 68 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults'
34 ]]></command>
35 <inputs>
36 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [required]" name="idistancematrix" optional="False" type="data"/>
37 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/>
38 <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1"/>
39 <param label="--p-palette: " name="ppalette" optional="True" type="select">
40 <option selected="True" value="None">Selection is Optional</option>
41 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
42 <option value="YellowOrangeRed">YellowOrangeRed</option>
43 <option value="OrangeRed">OrangeRed</option>
44 <option value="PurpleRed">PurpleRed</option>
45 <option value="RedPurple">RedPurple</option>
46 <option value="BluePurple">BluePurple</option>
47 <option value="GreenBlue">GreenBlue</option>
48 <option value="PurpleBlue">PurpleBlue</option>
49 <option value="YellowGreen">YellowGreen</option>
50 <option value="summer">summer</option>
51 <option value="copper">copper</option>
52 <option value="viridis">viridis</option>
53 <option value="plasma">plasma</option>
54 <option value="inferno">inferno</option>
55 <option value="magma">magma</option>
56 <option value="sirocco">sirocco</option>
57 <option value="drifting">drifting</option>
58 <option value="melancholy">melancholy</option>
59 <option value="enigma">enigma</option>
60 <option value="eros">eros</option>
61 <option value="spectre">spectre</option>
62 <option value="ambition">ambition</option>
63 <option value="mysteriousstains">mysteriousstains</option>
64 <option value="daydream">daydream</option>
65 <option value="solano">solano</option>
66 <option value="navarro">navarro</option>
67 <option value="dandelions">dandelions</option>
68 <option value="deepblue">deepblue</option>
69 <option value="verve">verve</option>
70 <option value="greyscale">greyscale</option>
71 </param>
72 69
73 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" /> 70 ]]></command>
71 <inputs>
72 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix a distance matrix [required]" name="idistancematrix" optional="False" type="data" />
73 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
74 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
75 </repeat>
76 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text" />
77 <param label="--p-k: INTEGER Number of nearest neighbors [default: 1]" name="pk" optional="True" type="integer" value="1" />
78 <param label="--p-palette: " name="ppalette" optional="True" type="select">
79 <option selected="True" value="None">Selection is Optional</option>
80 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
81 <option value="YellowOrangeRed">YellowOrangeRed</option>
82 <option value="OrangeRed">OrangeRed</option>
83 <option value="PurpleRed">PurpleRed</option>
84 <option value="RedPurple">RedPurple</option>
85 <option value="BluePurple">BluePurple</option>
86 <option value="GreenBlue">GreenBlue</option>
87 <option value="PurpleBlue">PurpleBlue</option>
88 <option value="YellowGreen">YellowGreen</option>
89 <option value="summer">summer</option>
90 <option value="copper">copper</option>
91 <option value="viridis">viridis</option>
92 <option value="cividis">cividis</option>
93 <option value="plasma">plasma</option>
94 <option value="inferno">inferno</option>
95 <option value="magma">magma</option>
96 <option value="sirocco">sirocco</option>
97 <option value="drifting">drifting</option>
98 <option value="melancholy">melancholy</option>
99 <option value="enigma">enigma</option>
100 <option value="eros">eros</option>
101 <option value="spectre">spectre</option>
102 <option value="ambition">ambition</option>
103 <option value="mysteriousstains">mysteriousstains</option>
104 <option value="daydream">daydream</option>
105 <option value="solano">solano</option>
106 <option value="navarro">navarro</option>
107 <option value="dandelions">dandelions</option>
108 <option value="deepblue">deepblue</option>
109 <option value="verve">verve</option>
110 <option value="greyscale">greyscale</option>
111 </param>
112 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
113
114 </inputs>
74 115
75 </inputs> 116 <outputs>
76 <outputs> 117 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" />
77 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/> 118 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.html" name="oaccuracyresults" />
78 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/> 119
79 </outputs> 120 </outputs>
80 <help><![CDATA[ 121
122 <help><![CDATA[
81 Run k-nearest-neighbors on a labeled distance matrix. 123 Run k-nearest-neighbors on a labeled distance matrix.
82 ##################################################### 124 ###############################################################
83 125
84 Run k-nearest-neighbors on a labeled distance matrix. Return cross- 126 Run k-nearest-neighbors on a labeled distance matrix. Return cross-
85 validated (leave one out) predictions and accuracy. k = 1 by default 127 validated (leave one out) predictions and accuracy. k = 1 by default
86 128
87 Parameters 129 Parameters
90 a distance matrix 132 a distance matrix
91 metadata : MetadataColumn[Categorical] 133 metadata : MetadataColumn[Categorical]
92 Categorical metadata column to use as prediction target. 134 Categorical metadata column to use as prediction target.
93 k : Int, optional 135 k : Int, optional
94 Number of nearest neighbors 136 Number of nearest neighbors
95 palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional 137 palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'cividis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
96 The color palette to use for plotting. 138 The color palette to use for plotting.
97 139
98 Returns 140 Returns
99 ------- 141 -------
100 predictions : SampleData[ClassifierPredictions] 142 predictions : SampleData[ClassifierPredictions]
101 leave one out predictions for each sample 143 leave one out predictions for each sample
102 accuracy_results : Visualization 144 accuracy_results : Visualization
103 Accuracy results visualization. 145 Accuracy results visualization.
104 ]]></help> 146 ]]></help>
105 <macros> 147 <macros>
106 <import>qiime_citation.xml</import> 148 <import>qiime_citation.xml</import>
107 </macros> 149 </macros>
108 <expand macro="qiime_citation"/> 150 <expand macro="qiime_citation"/>
109 </tool> 151 </tool>