Mercurial > repos > florianbegusch > qiime2_all

comparison qiime_feature-classifier_classify-sklearn.xml @ 0:09b7bcb72fa7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:09b7bcb72fa7
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>