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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2018.4">
+ − 3 <description> - De novo chimera filtering with vsearch.</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 qiime vsearch uchime-denovo --i-table=$itable --i-sequences=$isequences
+ − 10
+ − 11 #if $pdn:
+ − 12 --p-dn=$pdn
+ − 13 #end if
+ − 14 --o-nonchimeras=ononchimeras --o-stats=ostats --o-chimeras=ochimeras
+ − 15 #if $pmindiffs:
+ − 16 --p-mindiffs=$pmindiffs
+ − 17 #end if
+ − 18
+ − 19 #if $pminh:
+ − 20 --p-minh=$pminh
+ − 21 #end if
+ − 22
+ − 23 #if str($cmdconfig) != 'None':
+ − 24 --cmd-config=$cmdconfig
+ − 25 #end if
+ − 26
+ − 27 #if $pmindiv:
+ − 28 --p-mindiv=$pmindiv
+ − 29 #end if
+ − 30
+ − 31 #if $pxn:
+ − 32 --p-xn=$pxn
+ − 33 #end if
+ − 34 ;
+ − 35 cp ononchimeras.qza $ononchimeras;
+ − 36 cp ostats.qza $ostats;
+ − 37 cp ochimeras.qza $ochimeras;
+ − 38 ]]>
+ − 39 </command>
+ − 40 <inputs>
+ − 41 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
+ − 42 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
+ − 43
+ − 44 <param label="--p-dn: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" value="1.4"/>
+ − 45
+ − 46 <param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
+ − 47 <param label="--p-mindiv: Minimum divergence from closest parent. [default: 0.8]" name="pmindiv" optional="True" type="float" value="0.8"/>
+ − 48 <param label="--p-minh: Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" value="0.28"/>
+ − 49
+ − 50 <param label="--p-xn: No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" value="8.0"/>
+ − 51
+ − 52 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 53 </inputs>
+ − 54 <outputs>
+ − 55 <data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
+ − 56 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
+ − 57 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
+ − 58 </outputs>
+ − 59 <help>
+ − 60 <![CDATA[
+ − 61 De novo chimera filtering with vsearch.
+ − 62 ----------------------------------------
+ − 63
+ − 64 Apply the vsearch uchime_denovo method to identify chimeric feature
+ − 65 sequences. The results of this method can be used to filter chimeric
+ − 66 features from the corresponding feature table. For additional details,
+ − 67 please refer to the vsearch documentation.
+ − 68
+ − 69 Parameters
+ − 70 ----------
+ − 71 sequences : FeatureData[Sequence]
+ − 72 The feature sequences to be chimera-checked.
+ − 73 table : FeatureTable[Frequency]
+ − 74 Feature table (used for computing total feature abundances).
+ − 75 dn : Float % Range(0.0, None), optional
+ − 76 No vote pseudo-count, corresponding to the parameter n in the chimera
+ − 77 scoring function.
+ − 78 mindiffs : Int % Range(1, None), optional
+ − 79 Minimum number of differences per segment.
+ − 80 mindiv : Float % Range(0.0, None), optional
+ − 81 Minimum divergence from closest parent.
+ − 82 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ − 83 Minimum score (h). Increasing this value tends to reduce the number of
+ − 84 false positives and to decrease sensitivity.
+ − 85 xn : Float % Range(1.0, None, inclusive_start=False), optional
+ − 86 No vote weight, corresponding to the parameter beta in the scoring
+ − 87 function.
+ − 88
+ − 89 Returns
+ − 90 -------
+ − 91 chimeras : FeatureData[Sequence]
+ − 92 The chimeric sequences.
+ − 93 nonchimeras : FeatureData[Sequence]
+ − 94 The non-chimeric sequences.
+ − 95 stats : UchimeStats
+ − 96 Summary statistics from chimera checking.
+ − 97 ]]>
+ − 98 </help>
+ − 99 </tool>
