2
+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.4">
+ − 3 <description> - Reference-based 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-ref
+ − 9
+ − 10 --i-sequences=$isequences
+ − 11 --i-table=$itable
+ − 12 --i-reference-sequences=$ireferencesequences
+ − 13
4
+ − 14 #if str($pdn):
2
+ − 15 --p-dn=$pdn
+ − 16 #end if
+ − 17
4
+ − 18 #if str($pmindiffs):
2
+ − 19 --p-mindiffs=$pmindiffs
+ − 20 #end if
+ − 21
4
+ − 22 #if str($pmindiv):
2
+ − 23 --p-mindiv=$pmindiv
+ − 24 #end if
+ − 25
4
+ − 26 #if str($pminh):
2
+ − 27 --p-minh=$pminh
+ − 28 #end if
+ − 29
4
+ − 30 #if str($pxn):
2
+ − 31 --p-xn=$pxn
+ − 32 #end if
+ − 33
+ − 34 #set $pthreads = '${GALAXY_SLOTS:-4}'
+ − 35 #if str($pthreads):
+ − 36 --p-threads="$pthreads"
+ − 37 #end if
+ − 38
+ − 39 --o-chimeras=ochimeras
+ − 40 --o-nonchimeras=ononchimeras
+ − 41 --o-stats=ostats
+ − 42 ;
+ − 43 cp ochimeras.qza $ochimeras;
+ − 44 cp ononchimeras.qza $ononchimeras;
+ − 45 cp ostats.qza $ostats
+ − 46 ]]></command>
+ − 47 <inputs>
+ − 48 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
+ − 49 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
+ − 50 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>
+ − 51 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
+ − 52 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
+ − 53 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
+ − 54 <param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
+ − 55 <param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_min="True" value="8.0"/>
+ − 56 </inputs>
+ − 57 <outputs>
+ − 58 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
+ − 59 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
+ − 60 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
+ − 61 </outputs>
+ − 62 <help><![CDATA[
+ − 63 Reference-based chimera filtering with vsearch.
+ − 64 ###############################################
+ − 65
+ − 66 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
+ − 67 The results of this method can be used to filter chimeric features from the
+ − 68 corresponding feature table. For additional details, please refer to the
+ − 69 vsearch documentation.
+ − 70
+ − 71 Parameters
+ − 72 ----------
+ − 73 sequences : FeatureData[Sequence]
+ − 74 The feature sequences to be chimera-checked.
+ − 75 table : FeatureTable[Frequency]
+ − 76 Feature table (used for computing total feature abundances).
+ − 77 reference_sequences : FeatureData[Sequence]
+ − 78 The non-chimeric reference sequences.
+ − 79 dn : Float % Range(0.0, None), optional
+ − 80 No vote pseudo-count, corresponding to the parameter n in the chimera
+ − 81 scoring function.
+ − 82 mindiffs : Int % Range(1, None), optional
+ − 83 Minimum number of differences per segment.
+ − 84 mindiv : Float % Range(0.0, None), optional
+ − 85 Minimum divergence from closest parent.
+ − 86 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
+ − 87 Minimum score (h). Increasing this value tends to reduce the number of
+ − 88 false positives and to decrease sensitivity.
+ − 89 xn : Float % Range(1.0, None, inclusive_start=False), optional
+ − 90 No vote weight, corresponding to the parameter beta in the scoring
+ − 91 function.
+ − 92 threads : Int % Range(0, 256, inclusive_end=True), optional
+ − 93 The number of threads to use for computation. Passing 0 will launch one
+ − 94 thread per CPU core.
+ − 95
+ − 96 Returns
+ − 97 -------
+ − 98 chimeras : FeatureData[Sequence]
+ − 99 The chimeric sequences.
+ − 100 nonchimeras : FeatureData[Sequence]
+ − 101 The non-chimeric sequences.
+ − 102 stats : UchimeStats
+ − 103 Summary statistics from chimera checking.
+ − 104 ]]></help>
+ − 105 <macros>
+ − 106 <import>qiime_citation.xml</import>
+ − 107 </macros>
+ − 108 <expand macro="qiime_citation"/>
+ − 109 </tool>
