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comparison qiime2/qiime_feature-classifier_classify-consensus-vsearch.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path 18 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
19 --i-reference-taxonomy '$tax' 19 --i-reference-taxonomy '$tax'
20 #end if 20 #end if
21 21
22 22
23 #if $pmaxaccepts: 23
24 #if str($pmaxaccepts):
24 --p-maxaccepts=$pmaxaccepts 25 --p-maxaccepts=$pmaxaccepts
25 #end if 26 #end if
26 27
27 #if $ppercidentity: 28 #if str($ppercidentity):
28 --p-perc-identity=$ppercidentity 29 --p-perc-identity=$ppercidentity
29 #end if 30 #end if
30 31
31 #if $pquerycov: 32 #if str($pquerycov):
32 --p-query-cov=$pquerycov 33 --p-query-cov=$pquerycov
33 #end if 34 #end if
34 35
35 #if str($pstrand) != 'None': 36 #if str($pstrand) != 'None':
36 --p-strand=$pstrand 37 --p-strand=$pstrand
37 #end if 38 #end if
38 39
39 #if $pminconsensus: 40 #if str($pminconsensus):
40 --p-min-consensus=$pminconsensus 41 --p-min-consensus=$pminconsensus
42 #end if
43
44
45
46
47
48 #if '__sq__' in str($punassignablelabel):
49 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
50 #set $punassignablelabel = $punassignablelabel_temp
41 #end if 51 #end if
42 52
43 #if str($punassignablelabel): 53 #if str($punassignablelabel):
44 --p-unassignable-label="$punassignablelabel" 54 --p-unassignable-label="$punassignablelabel"
45 #end if 55 #end if
56
57
58
46 59
47 #set $pthreads = '${GALAXY_SLOTS:-4}' 60 #set $pthreads = '${GALAXY_SLOTS:-4}'
48 #if str($pthreads): 61 #if str($pthreads):
49 --p-threads="$pthreads" 62 --p-threads="$pthreads"
50 #end if 63 #end if
79 <option value="None">Selection is Optional</option> 92 <option value="None">Selection is Optional</option>
80 <option selected="True" value="both">both</option> 93 <option selected="True" value="both">both</option>
81 <option value="plus">plus</option> 94 <option value="plus">plus</option>
82 </param> 95 </param>
83 <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. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/> 96 <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. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
84 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/> 97 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
85 </inputs> 98 </inputs>
86 <outputs> 99 <outputs>
87 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> 100 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
88 </outputs> 101 </outputs>
89 <help><![CDATA[ 102 <help><![CDATA[