2
+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2019.4">
+ − 3 <description> - De novo chimera filtering with vsearch.</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2019.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime vsearch uchime-denovo
+ − 9
+ − 10 --i-sequences=$isequences
+ − 11 --i-table=$itable
+ − 12
+ − 13 #if $pdn:
+ − 14 --p-dn=$pdn
+ − 15 #end if
+ − 16
+ − 17 #if $pmindiffs:
+ − 18 --p-mindiffs=$pmindiffs
+ − 19 #end if
+ − 20
+ − 21 #if $pmindiv:
+ − 22 --p-mindiv=$pmindiv
+ − 23 #end if
+ − 24
+ − 25 #if $pminh:
+ − 26 --p-minh=$pminh
+ − 27 #end if
+ − 28
+ − 29 #if $pxn:
+ − 30 --p-xn=$pxn
+ − 31 #end if
+ − 32
+ − 33 --o-chimeras=ochimeras
+ − 34 --o-nonchimeras=ononchimeras
+ − 35 --o-stats=ostats
+ − 36 ;
+ − 37 cp ochimeras.qza $ochimeras;
+ − 38 cp ononchimeras.qza $ononchimeras;
+ − 39 cp ostats.qza $ostats
+ − 40 ]]></command>
+ − 41 <inputs>
+ − 42 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
+ − 43 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
+ − 44
+ − 45 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
+ − 46 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
+ − 47 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
+ − 48 <param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
+ − 49 <param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_max="True" value="8.0"/>
+ − 50 </inputs>
+ − 51 <outputs>
+ − 52 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
+ − 53 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
+ − 54 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
+ − 55 </outputs>
+ − 56 <help><![CDATA[
+ − 57 De novo chimera filtering with vsearch.
+ − 58 #######################################
+ − 59
+ − 60 Apply the vsearch uchime_denovo method to identify chimeric feature
+ − 61 sequences. The results of this method can be used to filter chimeric
+ − 62 features from the corresponding feature table. For additional details,
+ − 63 please refer to the vsearch documentation.
+ − 64
+ − 65 Parameters
+ − 66 ----------
+ − 67 sequences : FeatureData[Sequence]
+ − 68 The feature sequences to be chimera-checked.
+ − 69 table : FeatureTable[Frequency]
+ − 70 Feature table (used for computing total feature abundances).
+ − 71 dn : Float % Range(0.0, None), optional
+ − 72 No vote pseudo-count, corresponding to the parameter n in the chimera
+ − 73 scoring function.
+ − 74 mindiffs : Int % Range(1, None), optional
+ − 75 Minimum number of differences per segment.
+ − 76 mindiv : Float % Range(0.0, None), optional
+ − 77 Minimum divergence from closest parent.
+ − 78 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ − 79 Minimum score (h). Increasing this value tends to reduce the number of
+ − 80 false positives and to decrease sensitivity.
+ − 81 xn : Float % Range(1.0, None, inclusive_start=False), optional
+ − 82 No vote weight, corresponding to the parameter beta in the scoring
+ − 83 function.
+ − 84
+ − 85 Returns
+ − 86 -------
+ − 87 chimeras : FeatureData[Sequence]
+ − 88 The chimeric sequences.
+ − 89 nonchimeras : FeatureData[Sequence]
+ − 90 The non-chimeric sequences.
+ − 91 stats : UchimeStats
+ − 92 Summary statistics from chimera checking.
+ − 93 ]]></help>
+ − 94 <macros>
+ − 95 <import>qiime_citation.xml</import>
+ − 96 </macros>
+ − 97 <expand macro="qiime_citation"/>
+ − 98 </tool>
