annotate qiime2/qiime_feature-classifier_classify-sklearn.xml @ 12:33e7a3470046 draft

Deleted selected files
author florianbegusch
date Thu, 03 Sep 2020 09:44:28 +0000
parents f190567fe3f6
children a0a8d77a991c
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" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 6
diff changeset
2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Pre-fitted sklearn-based taxonomy classifier</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 6
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
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
6
florianbegusch
parents: 0
diff changeset
10
florianbegusch
parents: 0
diff changeset
11 #if str( $id_to_classifier_fp.selector ) == 'history'
florianbegusch
parents: 0
diff changeset
12 #set $classifier = $id_to_classifier_fp.classifier_fp
florianbegusch
parents: 0
diff changeset
13 --i-classifier '$classifier'
florianbegusch
parents: 0
diff changeset
14 #else:
florianbegusch
parents: 0
diff changeset
15 #set $classifier = $id_to_classifier_fp.classifier_fp.fields.path
florianbegusch
parents: 0
diff changeset
16 --i-classifier '$classifier'
florianbegusch
parents: 0
diff changeset
17 #end if
florianbegusch
parents: 0
diff changeset
18
florianbegusch
parents: 0
diff changeset
19
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 --i-reads=$ireads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 #set $pnjobs = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 #if str($pnjobs):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 --p-n-jobs="$pnjobs"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
6
florianbegusch
parents: 0
diff changeset
29 #if str($pconfidence) != '':
florianbegusch
parents: 0
diff changeset
30 #if float($pconfidence) >= 0.0:
florianbegusch
parents: 0
diff changeset
31 --p-confidence=$pconfidence
florianbegusch
parents: 0
diff changeset
32 #end if
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 #if str($preadorientation) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 --p-read-orientation=$preadorientation
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 --o-classification=oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 cp oclassification.qza $oclassification
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <inputs>
6
florianbegusch
parents: 0
diff changeset
44 <conditional name="id_to_classifier_fp" optional="True">
florianbegusch
parents: 0
diff changeset
45 <param name="selector" type="select" label="Reference classifier to query">
florianbegusch
parents: 0
diff changeset
46 <option value="cached">Public classifiers</option>
florianbegusch
parents: 0
diff changeset
47 <option value="history">Classifiers from your history</option>
florianbegusch
parents: 0
diff changeset
48 </param>
florianbegusch
parents: 0
diff changeset
49 <when value="cached">
florianbegusch
parents: 0
diff changeset
50 <param name="classifier_fp" label="Reference classifier" type="select" optional="True">
florianbegusch
parents: 0
diff changeset
51 <options from_data_table="qiime_rep_set" />
florianbegusch
parents: 0
diff changeset
52 </param>
florianbegusch
parents: 0
diff changeset
53 </when>
florianbegusch
parents: 0
diff changeset
54 <when value="history">
florianbegusch
parents: 0
diff changeset
55 <param name="classifier_fp" type="data" format="qza,no_unzip.zip" label="Reference classifier" optional="True" />
florianbegusch
parents: 0
diff changeset
56 </when>
florianbegusch
parents: 0
diff changeset
57 </conditional>
florianbegusch
parents: 0
diff changeset
58
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 <option value="same">same</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 <option value="reverse-complement">reverse-complement</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 Pre-fitted sklearn-based taxonomy classifier
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 ############################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 Classify reads by taxon using a fitted classifier.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 reads : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 The feature data to be classified.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 classifier : TaxonomicClassifier
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 The taxonomic classifier for classifying the reads.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 reads_per_batch : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 Number of reads to process in each batch. If 0, this parameter is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 autoscaled to min( number of query sequences / n_jobs, 20000).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 pre_dispatch : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 to be pre-dispatched.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 confidence : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 Confidence threshold for limiting taxonomic depth. Provide -1 to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 disable confidence calculation, or 0 to calculate confidence but not
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 apply it to limit the taxonomic depth of the assignments.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 read_orientation : Str % Choices('same', 'reverse-complement'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 Direction of reads with respect to reference sequences. same will cause
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 reads to be classified unchanged; reverse-complement will cause reads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 to be reversed and complemented prior to classification. Default is to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 autodetect based on the confidence estimates for the first 100 reads.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 classification : FeatureData[Taxonomy]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106 </tool>