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comparison qiime2/qiime_feature-classifier_classify-sklearn.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_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.7"> 2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn"
3 <description> - Pre-fitted sklearn-based taxonomy classifier</description> 3 version="2020.8">
4 <requirements> 4 <description>Pre-fitted sklearn-based taxonomy classifier</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 feature-classifier classify-sklearn 9 qiime feature-classifier classify-sklearn
9
10
11 #if str( $id_to_classifier_fp.selector ) == 'history'
12 #set $classifier = $id_to_classifier_fp.classifier_fp
13 --i-classifier '$classifier'
14 #else:
15 #set $classifier = $id_to_classifier_fp.classifier_fp.fields.path
16 --i-classifier '$classifier'
17 #end if
18
19 10
20 --i-reads=$ireads 11 --i-reads=$ireads
21 12
22 #set $pnjobs = '${GALAXY_SLOTS:-4}' 13 --i-classifier=$iclassifier
23 14
24 #if str($pnjobs): 15 --p-n-jobs=$pnjobs
25 --p-n-jobs="$pnjobs"
26 #end if
27 16
28 17 #if str($pconfidence) != 'None':
29 #if str($pconfidence) != '': 18 --p-confidence=$pconfidence
30 #if float($pconfidence) >= 0.0:
31 --p-confidence=$pconfidence
32 #end if
33 #end if 19 #end if
34 20
35 #if str($preadorientation) != 'None': 21 #if str($preadorientation) != 'None':
36 --p-read-orientation=$preadorientation 22 --p-read-orientation=$preadorientation
37 #end if 23 #end if
38 24
39 --o-classification=oclassification 25 --o-classification=oclassification
26
27 #if str($examples) != 'None':
28 --examples=$examples
29 #end if
30
40 ; 31 ;
41 cp oclassification.qza $oclassification 32 cp oclassification.qza $oclassification
42 ]]></command>
43 <inputs>
44 <conditional name="id_to_classifier_fp" optional="True">
45 <param name="selector" type="select" label="Reference classifier to query">
46 <option value="cached">Public classifiers</option>
47 <option value="history">Classifiers from your history</option>
48 </param>
49 <when value="cached">
50 <param name="classifier_fp" label="Reference classifier" type="select" optional="True">
51 <options from_data_table="qiime_rep_set" />
52 </param>
53 </when>
54 <when value="history">
55 <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" />
56 </when>
57 </conditional>
58 33
59 <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data"/> 34 ]]></command>
60 <param label="--p-confidence: NUMBER Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments. [default: 0.7]" name="pconfidence" optional="True" type="float" value="0.7"/> 35 <inputs>
61 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select"> 36 <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data" />
62 <option selected="True" value="None">Selection is Optional</option> 37 <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier The taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data" />
63 <option value="same">same</option> 38 <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
64 <option value="reverse-complement">reverse-complement</option> 39 <option selected="True" value="None">Selection is Optional</option>
65 </param> 40 <option value="Float % Range(0">Float % Range(0</option>
66 </inputs> 41 <option value="1">1</option>
67 <outputs> 42 <option value="inclusive_end=True">inclusive_end=True</option>
68 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> 43 </param>
69 </outputs> 44 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
70 <help><![CDATA[ 45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="same">same</option>
47 <option value="reverse-complement">reverse-complement</option>
48 <option value="auto">auto</option>
49 </param>
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
51
52 </inputs>
53
54 <outputs>
55 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
56
57 </outputs>
58
59 <help><![CDATA[
71 Pre-fitted sklearn-based taxonomy classifier 60 Pre-fitted sklearn-based taxonomy classifier
72 ############################################ 61 ###############################################################
73 62
74 Classify reads by taxon using a fitted classifier. 63 Classify reads by taxon using a fitted classifier.
75 64
76 Parameters 65 Parameters
77 ---------- 66 ----------
78 reads : FeatureData[Sequence] 67 reads : FeatureData[Sequence]
79 The feature data to be classified. 68 The feature data to be classified.
80 classifier : TaxonomicClassifier 69 classifier : TaxonomicClassifier
81 The taxonomic classifier for classifying the reads. 70 The taxonomic classifier for classifying the reads.
82 reads_per_batch : Int % Range(0, None), optional 71 reads_per_batch : Int % Range(0, None), optional
83 Number of reads to process in each batch. If 0, this parameter is 72 Number of reads to process in each batch. If "auto", this parameter is
84 autoscaled to min( number of query sequences / n_jobs, 20000). 73 autoscaled to min( number of query sequences / n_jobs, 20000).
74 n_jobs : Int, optional
75 The maximum number of concurrently worker processes. If -1 all CPUs are
76 used. If 1 is given, no parallel computing code is used at all, which
77 is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are
78 used. Thus for n_jobs = -2, all CPUs but one are used.
85 pre_dispatch : Str, optional 79 pre_dispatch : Str, optional
86 "all" or expression, as in "3*n_jobs". The number of batches (of tasks) 80 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
87 to be pre-dispatched. 81 to be pre-dispatched.
88 confidence : Float, optional 82 confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional
89 Confidence threshold for limiting taxonomic depth. Provide -1 to 83 Confidence threshold for limiting taxonomic depth. Set to "disable" to
90 disable confidence calculation, or 0 to calculate confidence but not 84 disable confidence calculation, or 0 to calculate confidence but not
91 apply it to limit the taxonomic depth of the assignments. 85 apply it to limit the taxonomic depth of the assignments.
92 read_orientation : Str % Choices('same', 'reverse-complement'), optional 86 read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional
93 Direction of reads with respect to reference sequences. same will cause 87 Direction of reads with respect to reference sequences. same will cause
94 reads to be classified unchanged; reverse-complement will cause reads 88 reads to be classified unchanged; reverse-complement will cause reads
95 to be reversed and complemented prior to classification. Default is to 89 to be reversed and complemented prior to classification. "auto" will
96 autodetect based on the confidence estimates for the first 100 reads. 90 autodetect orientation based on the confidence estimates for the first
91 100 reads.
97 92
98 Returns 93 Returns
99 ------- 94 -------
100 classification : FeatureData[Taxonomy] 95 classification : FeatureData[Taxonomy]
101 ]]></help> 96 ]]></help>
102 <macros> 97 <macros>
103 <import>qiime_citation.xml</import> 98 <import>qiime_citation.xml</import>
104 </macros> 99 </macros>
105 <expand macro="qiime_citation"/> 100 <expand macro="qiime_citation"/>
106 </tool> 101 </tool>