Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_sample-classifier_classify-samples-from-dist.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
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13:887cd4ad8e16 | 14:a0a8d77a991c |
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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> |