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

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
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5:a025a4a89e07 6:de4c22a52df4
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-hybrid-vsearch-sklearn" name="qiime feature-classifier classify-hybrid-vsearch-sklearn" version="2019.7">
3 <description> - ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier</description>
4 <requirements>
5 <requirement type="package" version="2019.7">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier classify-hybrid-vsearch-sklearn
9
10 --i-query=$iquery
11 --i-reference-reads=$ireferencereads
12 --i-reference-taxonomy=$ireferencetaxonomy
13 --i-classifier=$iclassifier
14
15 #if str($pmaxaccepts) != 'None':
16 --p-maxaccepts=$pmaxaccepts
17 #end if
18
19 #if str($ppercidentity):
20 --p-perc-identity=$ppercidentity
21 #end if
22
23 #if str($pquerycov):
24 --p-query-cov=$pquerycov
25 #end if
26
27 #if str($pstrand) != 'None':
28 --p-strand=$pstrand
29 #end if
30
31 #if str($pminconsensus):
32 --p-min-consensus=$pminconsensus
33 #end if
34
35 #if str($pconfidence) != 'None':
36 --p-confidence=$pconfidence
37 #end if
38
39 #if str($preadorientation) != 'None':
40 --p-read-orientation=$preadorientation
41 #end if
42
43 #set $pthreads = '${GALAXY_SLOTS:-4}'
44
45 #if str($pthreads):
46
47 #if str($pthreads):
48 --p-threads="$pthreads"
49 #end if
50
51 #end if
52
53
54 #if $pprefilter:
55 --p-prefilter
56 #end if
57
58 #if str($psamplesize):
59 --p-sample-size=$psamplesize
60 #end if
61
62 #if str($prandseed):
63 --p-randseed=$prandseed
64 #end if
65
66
67 --o-classification=oclassification
68
69 ;
70 cp oclassification.qza $oclassification
71 ]]></command>
72 <inputs>
73 <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically. [required]" name="iquery" optional="False" type="data"/>
74 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences. [required]" name="ireferencereads" optional="False" type="data"/>
75 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels. [required]" name="ireferencetaxonomy" optional="False" type="data"/>
76 <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier Pre-trained sklearn taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data"/>
77 <param label="--p-maxaccepts: " name="pmaxaccepts" optional="True" type="select">
78 <option selected="True" value="None">Selection is Optional</option>
79 <option value="Int % Range(1">Int % Range(1</option>
80 <option value="None">None</option>
81 </param>
82 <param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Percent sequence similarity to use for PREFILTER. Reject match if percent identity to query is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.5]" name="ppercidentity" optional="True" type="float" value="0.5"/>
83 <param label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Query coverage threshold to use for PREFILTER. Reject match if query alignment coverage per high-scoring pair is lower. Set to a lower value to perform a rough pre-filter. This parameter is ignored if `prefilter` is disabled. [default: 0.8]" name="pquerycov" optional="True" type="float" value="0.8"/>
84 <param label="--p-strand: " name="pstrand" optional="True" type="select">
85 <option selected="True" value="None">Selection is Optional</option>
86 <option value="both">both</option>
87 <option value="plus">plus</option>
88 </param>
89 <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. [default: 0.51]" name="pminconsensus" optional="True" type="float" value="0.51"/>
90 <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
91 <option selected="True" value="None">Selection is Optional</option>
92 <option value="Float % Range(0">Float % Range(0</option>
93 <option value="1">1</option>
94 <option value="inclusive_end=True">inclusive_end=True</option>
95 </param>
96 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
97 <option selected="True" value="None">Selection is Optional</option>
98 <option value="same">same</option>
99 <option value="reverse-complement">reverse-complement</option>
100 <option value="auto">auto</option>
101 </param>
102 <param label="--p-prefilter: --p-no-prefilter Toggle positive filter of query sequences on or off. [default: True]" name="pprefilter" selected="False" type="boolean"/>
103 <param label="--p-sample-size: INTEGER Range(1, None) Randomly extract the given number of sequences from the reference database to use for prefiltering. This parameter is ignored if `prefilter` is disabled. [default: 1000]" name="psamplesize" optional="True" type="integer" value="1000"/>
104 <param label="--p-randseed: INTEGER Use integer as a seed for the pseudo-random generator Range(0, None) used during prefiltering. A given seed always produces the same output, which is useful for replicability. Set to 0 to use a pseudo-random seed. This parameter is ignored if `prefilter` is disabled. [default: 0]" name="prandseed" optional="True" type="integer" value="0"/>
105 </inputs>
106 <outputs>
107 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
108 </outputs>
109 <help><![CDATA[
110
111 ]]></help>
112 <macros>
113 <import>qiime_citation.xml</import>
114 </macros>
115 <expand macro="qiime_citation"/>
116 </tool>