|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2018.4">
|
|
|
3 <description>- Pre-fitted sklearn-based taxonomy classifier</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime feature-classifier classify-sklearn
|
|
|
9
|
|
|
10 #if str( $id_to_classifier_fp.selector ) == 'history'
|
|
|
11 #set $classifier = $id_to_classifier_fp.classifier_fp
|
|
|
12 --i-classifier '$classifier'
|
|
|
13 #else:
|
|
|
14 #set $classifier = $id_to_classifier_fp.classifier.fields.path
|
|
|
15 --i-classifier '$classifier'
|
|
|
16 #end if
|
|
|
17
|
|
|
18 --i-reads=$ireads
|
|
|
19
|
|
|
20 #if str($pconfidence) != '':
|
|
|
21 #if float($pconfidence) >= 0.0:
|
|
|
22 --p-confidence=$pconfidence
|
|
|
23 #end if
|
|
|
24 #end if
|
|
|
25
|
|
|
26 #if str($preadorientation) != 'None':
|
|
|
27 --p-read-orientation=$preadorientation
|
|
|
28 #end if
|
|
|
29
|
|
|
30 #if str($cmdconfig) != 'None':
|
|
|
31 --cmd-config=$cmdconfig
|
|
|
32 #end if
|
|
|
33
|
|
|
34 #set $pnjobs = '${GALAXY_SLOTS:-4}'
|
|
|
35 --p-n-jobs="$pnjobs"
|
|
|
36 --o-classification=oclassification;
|
|
|
37
|
|
|
38 cp oclassification.qza $oclassification;
|
|
|
39 ]]></command>
|
|
|
40 <inputs>
|
|
|
41 <param format="qza,no_unzip.zip" label="--i-reads: FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data"/>
|
|
|
42
|
|
|
43 <conditional name="id_to_classifier_fp" optional="True">
|
|
|
44 <param name="selector" type="select" label="Reference classifier to query">
|
|
|
45 <option value="cached">Public classifiers</option>
|
|
|
46 <option value="history">Classifiers from your history</option>
|
|
|
47 </param>
|
|
|
48 <when value="cached">
|
|
|
49 <param name="classifier_fp" label="Reference classifier" type="select" optional="True">
|
|
|
50 <options from_data_table="qiime_taxonomy" />
|
|
|
51 </param>
|
|
|
52 </when>
|
|
|
53 <when value="history">
|
|
|
54 <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" />
|
|
|
55 </when>
|
|
|
56 </conditional>
|
|
|
57
|
|
|
58 <param label="--p-confidence: 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"/>
|
|
|
59 <param label="--p-read-orientation: [reverse-complement|same] Direction of reads with respect to reference sequences. same will cause reads to be classified unchanged; reverse-complement will cause reads to be reversed and complemented prior to classification. Default is to autodetect based on the confidence estimates for the first 100 reads. [optional]" name="preadorientation" optional="True" type="select">
|
|
|
60 <option selected="True" value="None">Selection is Optional</option>
|
|
|
61 <option value="reverse-complement">reverse-complement</option>
|
|
|
62 <option value="same">same</option>
|
|
|
63 </param>
|
|
|
64 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
65 </inputs>
|
|
|
66 <outputs>
|
|
|
67 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
|
|
|
68 </outputs>
|
|
|
69 <help><![CDATA[
|
|
|
70 Pre-fitted sklearn-based taxonomy classifier
|
|
|
71 ---------------------------------------------
|
|
|
72
|
|
|
73 Classify reads by taxon using a fitted classifier.
|
|
|
74
|
|
|
75 Parameters
|
|
|
76 ----------
|
|
|
77 reads : FeatureData[Sequence]
|
|
|
78 The feature data to be classified.
|
|
|
79 classifier : TaxonomicClassifier
|
|
|
80 The taxonomic classifier for classifying the reads.
|
|
|
81 reads_per_batch : Int % Range(0, None), optional
|
|
|
82 Number of reads to process in each batch. If 0, this parameter is
|
|
|
83 autoscaled to the number of query sequences / n_jobs.
|
|
|
84 pre_dispatch : Str, optional
|
|
|
85 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
|
|
|
86 to be pre-dispatched.
|
|
|
87 confidence : Float, optional
|
|
|
88 Confidence threshold for limiting taxonomic depth. Provide -1 to
|
|
|
89 disable confidence calculation, or 0 to calculate confidence but not
|
|
|
90 apply it to limit the taxonomic depth of the assignments.
|
|
|
91 read_orientation : Str % Choices({'reverse-complement', 'same'}), optional
|
|
|
92 Direction of reads with respect to reference sequences. same will cause
|
|
|
93 reads to be classified unchanged; reverse-complement will cause reads
|
|
|
94 to be reversed and complemented prior to classification. Default is to
|
|
|
95 autodetect based on the confidence estimates for the first 100 reads.
|
|
|
96
|
|
|
97 Returns
|
|
|
98 -------
|
|
|
99 classification : FeatureData[Taxonomy]
|
|
|
100 ]]>
|
|
|
101 </help>
|
|
|
102 </tool>
|
