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comparison qiime2/qiime_feature-classifier_classify-consensus-blast.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
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path 17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
18 --i-reference-taxonomy '$tax' 18 --i-reference-taxonomy '$tax'
19 #end if 19 #end if
20 20
21 21
22 #if $pmaxaccepts: 22 #if str($pmaxaccepts):
23 --p-maxaccepts=$pmaxaccepts 23 --p-maxaccepts=$pmaxaccepts
24 #end if 24 #end if
25 25
26 #if $ppercidentity: 26 #if str($ppercidentity):
27 --p-perc-identity=$ppercidentity 27 --p-perc-identity=$ppercidentity
28 #end if 28 #end if
29 29
30 #if $pquerycov: 30 #if str($pquerycov):
31 --p-query-cov=$pquerycov 31 --p-query-cov=$pquerycov
32 #end if 32 #end if
33 33
34 #if str($pstrand) != 'None': 34 #if str($pstrand) != 'None':
35 --p-strand=$pstrand 35 --p-strand=$pstrand
36 #end if 36 #end if
37 37
38 #if $pevalue: 38 #if str($pevalue):
39 --p-evalue=$pevalue 39 --p-evalue=$pevalue
40 #end if 40 #end if
41 41
42 #if $pminconsensus: 42 #if str($pminconsensus):
43 --p-min-consensus=$pminconsensus 43 --p-min-consensus=$pminconsensus
44 #end if
45
46
47
48
49
50 #if '__sq__' in str($punassignablelabel):
51 #set $punassignablelabel_temp = $punassignablelabel.replace('__sq__', "'")
52 #set $punassignablelabel = $punassignablelabel_temp
44 #end if 53 #end if
45 54
46 #if str($punassignablelabel): 55 #if str($punassignablelabel):
47 --p-unassignable-label="$punassignablelabel" 56 --p-unassignable-label="$punassignablelabel"
48 #end if 57 #end if
58
59
49 60
50 --o-classification=oclassification 61 --o-classification=oclassification
51 ; 62 ;
52 cp oclassification.qza $oclassification 63 cp oclassification.qza $oclassification
53 ]]></command> 64 ]]></command>
79 <option value="plus">plus</option> 90 <option value="plus">plus</option>
80 <option value="minus">minus</option> 91 <option value="minus">minus</option>
81 </param> 92 </param>
82 <param label="--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/> 93 <param label="--p-evalue: NUMBER BLAST expectation value (E) threshold for saving hits. [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001"/>
83 <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/> 94 <param label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True) Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0]. [default: 0.51]" name="pminconsensus" optional="True" type="float" min="0.5" max="1" exclude_min="True" exclude_max="False" value="0.51"/>
84 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="'Unassigned'"/> 95 <param label="--p-unassignable-label: TEXT [default: 'Unassigned']" name="punassignablelabel" optional="True" type="text" value="Unassigned"/>
85 </inputs> 96 </inputs>
86 <outputs> 97 <outputs>
87 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/> 98 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
88 </outputs> 99 </outputs>
89 <help><![CDATA[ 100 <help><![CDATA[