annotate qiime2/qiime_feature-classifier_classify-sklearn.xml @ 5:a025a4a89e07 draft

Uploaded
author florianbegusch
date Mon, 05 Aug 2019 01:29:30 -0400
parents 370e0b6e9826
children de4c22a52df4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Pre-fitted sklearn-based taxonomy classifier</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime feature-classifier classify-sklearn
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-reads=$ireads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-classifier=$iclassifier
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 #set $pnjobs = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #if str($pnjobs):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 --p-n-jobs="$pnjobs"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #if $pconfidence:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 --p-confidence=$pconfidence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 #if str($preadorientation) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 --p-read-orientation=$preadorientation
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 --o-classification=oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 cp oclassification.qza $oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier The taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <param label="--p-confidence: NUMBER Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments. [default: 0.7]" name="pconfidence" optional="True" type="float" value="0.7"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 <option value="same">same</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <option value="reverse-complement">reverse-complement</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 Pre-fitted sklearn-based taxonomy classifier
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 ############################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 Classify reads by taxon using a fitted classifier.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 reads : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 The feature data to be classified.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 classifier : TaxonomicClassifier
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 The taxonomic classifier for classifying the reads.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 reads_per_batch : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 Number of reads to process in each batch. If 0, this parameter is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 autoscaled to min( number of query sequences / n_jobs, 20000).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 pre_dispatch : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 to be pre-dispatched.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 confidence : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 Confidence threshold for limiting taxonomic depth. Provide -1 to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 disable confidence calculation, or 0 to calculate confidence but not
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 apply it to limit the taxonomic depth of the assignments.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 read_orientation : Str % Choices('same', 'reverse-complement'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 Direction of reads with respect to reference sequences. same will cause
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 reads to be classified unchanged; reverse-complement will cause reads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 to be reversed and complemented prior to classification. Default is to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 autodetect based on the confidence estimates for the first 100 reads.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 classification : FeatureData[Taxonomy]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 </tool>