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comparison qiime2/qiime_sample-classifier_metatable.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_metatable" name="qiime sample-classifier metatable" version="2019.7"> 2 <tool id="qiime_sample-classifier_metatable" name="qiime sample-classifier metatable"
3 <description> - Convert (and merge) positive numeric metadata (in)to feature table.</description> 3 version="2020.8">
4 <requirements> 4 <description>Convert (and merge) positive numeric metadata (in)to feature table.</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 metatable 9 qiime sample-classifier metatable
9 10
10
11 #if str($itable) != 'None': 11 #if str($itable) != 'None':
12 --i-table=$itable 12 --i-table=$itable
13 #end if 13 #end if
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
14 24
15 #if str($pmissingsamples) != 'None': 25 #if str($pmissingsamples) != 'None':
16 --p-missing-samples=$pmissingsamples 26 --p-missing-samples=$pmissingsamples
17 #end if 27 #end if
18 28
19 #if str($pmissingvalues) != 'None': 29 #if str($pmissingvalues) != 'None':
20 --p-missing-values=$pmissingvalues 30 --p-missing-values=$pmissingvalues
21 #end if 31 #end if
22 32
23 33 #if $pdropallunique:
24 #if $input_files_mmetadatafile: 34 --p-drop-all-unique
25 #def list_dict_to_string(list_dict):
26 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
27 #for d in list_dict[1:]:
28 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
29 #end for
30 #return $file_list
31 #end def
32 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
33 #end if 35 #end if
34 36
37 --o-converted-table=oconvertedtable
35 38
36 --o-converted-table=oconvertedtable 39 #if str($examples) != 'None':
40 --examples=$examples
41 #end if
42
37 ; 43 ;
38 cp oconvertedtable.qza $oconvertedtable 44 cp oconvertedtable.qza $oconvertedtable
39 ]]></command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [optional]" name="itable" optional="True" type="data"/>
42 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
43 <option selected="True" value="None">Selection is Optional</option>
44 <option value="error">error</option>
45 <option value="ignore">ignore</option>
46 </param>
47 <param label="--p-missing-values: " name="pmissingvalues" optional="True" type="select">
48 <option selected="True" value="None">Selection is Optional</option>
49 <option value="drop_samples">drop_samples</option>
50 <option value="drop_features">drop_features</option>
51 <option value="error">error</option>
52 <option value="fill">fill</option>
53 </param>
54 45
55 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> 46 ]]></command>
56 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" /> 47 <inputs>
57 </repeat> 48 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [optional]" name="itable" optional="False" type="data" />
49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
50 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Metadata file to convert to feature table. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
51 </repeat>
52 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="error">error</option>
55 <option value="ignore">ignore</option>
56 </param>
57 <param label="--p-missing-values: " name="pmissingvalues" optional="True" type="select">
58 <option selected="True" value="None">Selection is Optional</option>
59 <option value="drop_samples">drop_samples</option>
60 <option value="drop_features">drop_features</option>
61 <option value="error">error</option>
62 <option value="fill">fill</option>
63 </param>
64 <param label="--p-drop-all-unique: --p-drop-all-unique: / --p-no-drop-all-unique If True, columns that contain a unique value for every ID will be dropped. [default: False]" name="pdropallunique" selected="False" type="boolean" />
65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
66
67 </inputs>
58 68
59 </inputs> 69 <outputs>
60 <outputs> 70 <data format="qza" label="${tool.name} on ${on_string}: convertedtable.qza" name="oconvertedtable" />
61 <data format="qza" label="${tool.name} on ${on_string}: convertedtable.qza" name="oconvertedtable"/> 71
62 </outputs> 72 </outputs>
63 <help><![CDATA[ 73
74 <help><![CDATA[
64 Convert (and merge) positive numeric metadata (in)to feature table. 75 Convert (and merge) positive numeric metadata (in)to feature table.
65 ################################################################### 76 ###############################################################
66 77
67 Convert numeric sample metadata from TSV file into a feature table. 78 Convert numeric sample metadata from TSV file into a feature table.
68 Optionally merge with an existing feature table. Only numeric metadata will 79 Optionally merge with an existing feature table. Only numeric metadata will
69 be converted; categorical columns will be silently dropped. By default, if 80 be converted; categorical columns will be silently dropped. By default, if
70 a table is used as input only samples found in both the table and metadata 81 a table is used as input only samples found in both the table and metadata
71 (intersection) are merged, and others are silently dropped. Set 82 (intersection) are merged, and others are silently dropped. Set
72 missing_samples="error" to raise an error if samples found in the table are 83 missing_samples="error" to raise an error if samples found in the table are
73 missing from the metadata file. The metadata file can always contain a 84 missing from the metadata file. The metadata file can always contain a
74 superset of samples. Note that columns will be dropped if they are non- 85 superset of samples. Note that columns will be dropped if they are non-
75 numeric, contain only unique values, contain no unique values (zero 86 numeric, contain no unique values (zero variance), contain only empty
76 variance), contain only empty cells, or contain negative values. This 87 cells, or contain negative values. This method currently only converts
77 method currently only converts postive numeric metadata into feature data. 88 postive numeric metadata into feature data. Tip: convert categorical
78 Tip: convert categorical columns to dummy variables to include them in the 89 columns to dummy variables to include them in the output feature table.
79 output feature table.
80 90
81 Parameters 91 Parameters
82 ---------- 92 ----------
83 metadata : Metadata 93 metadata : Metadata
84 Metadata file to convert to feature table. 94 Metadata file to convert to feature table.
92 retained. 102 retained.
93 missing_values : Str % Choices('drop_samples', 'drop_features', 'error', 'fill'), optional 103 missing_values : Str % Choices('drop_samples', 'drop_features', 'error', 'fill'), optional
94 How to handle missing values (nans) in metadata. Either "drop_samples" 104 How to handle missing values (nans) in metadata. Either "drop_samples"
95 with missing values, "drop_features" with missing values, "fill" 105 with missing values, "drop_features" with missing values, "fill"
96 missing values with zeros, or "error" if any missing values are found. 106 missing values with zeros, or "error" if any missing values are found.
107 drop_all_unique : Bool, optional
108 If True, columns that contain a unique value for every ID will be
109 dropped.
97 110
98 Returns 111 Returns
99 ------- 112 -------
100 converted_table : FeatureTable[Frequency] 113 converted_table : FeatureTable[Frequency]
101 Converted feature table 114 Converted feature table
102 ]]></help> 115 ]]></help>
103 <macros> 116 <macros>
104 <import>qiime_citation.xml</import> 117 <import>qiime_citation.xml</import>
105 </macros> 118 </macros>
106 <expand macro="qiime_citation"/> 119 <expand macro="qiime_citation"/>
107 </tool> 120 </tool>