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comparison qiime2/qiime_feature-classifier_classify-sklearn.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime feature-classifier classify-sklearn 8 qiime feature-classifier classify-sklearn
9 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 --i-reads=$ireads 20 --i-reads=$ireads
11 --i-classifier=$iclassifier
12 21
13 #set $pnjobs = '${GALAXY_SLOTS:-4}' 22 #set $pnjobs = '${GALAXY_SLOTS:-4}'
14 23
15 #if str($pnjobs): 24 #if str($pnjobs):
16 --p-n-jobs="$pnjobs" 25 --p-n-jobs="$pnjobs"
17 #end if 26 #end if
18 27
19 28
20 #if $pconfidence: 29 #if str($pconfidence) != '':
21 --p-confidence=$pconfidence 30 #if float($pconfidence) >= 0.0:
31 --p-confidence=$pconfidence
32 #end if
22 #end if 33 #end if
23 34
24 #if str($preadorientation) != 'None': 35 #if str($preadorientation) != 'None':
25 --p-read-orientation=$preadorientation 36 --p-read-orientation=$preadorientation
26 #end if 37 #end if
28 --o-classification=oclassification 39 --o-classification=oclassification
29 ; 40 ;
30 cp oclassification.qza $oclassification 41 cp oclassification.qza $oclassification
31 ]]></command> 42 ]]></command>
32 <inputs> 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 <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"/> 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 <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"/>
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"/> 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"/>
36 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select"> 61 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
37 <option selected="True" value="None">Selection is Optional</option> 62 <option selected="True" value="None">Selection is Optional</option>
38 <option value="same">same</option> 63 <option value="same">same</option>
39 <option value="reverse-complement">reverse-complement</option> 64 <option value="reverse-complement">reverse-complement</option>