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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2018.4">
+ − 3 <description> - Deblur sequences using a user-specified positive filter.</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime deblur denoise-other --i-demultiplexed-seqs=$idemultiplexedseqs --p-trim-length="$ptrimlength" --i-reference-seqs=$ireferenceseqs
+ − 9
+ − 10 #if str($cmdconfig) != 'None':
+ − 11 --cmd-config=$cmdconfig
+ − 12 #end if
+ − 13
+ − 14 #if $phashedfeatureids:
+ − 15 --p-hashed-feature-ids
+ − 16 #else
+ − 17 --p-no-hashed-feature-ids
+ − 18 #end if
+ − 19
+ − 20 #if $pindelprob:
+ − 21 --p-indel-prob=$pindelprob
+ − 22 #end if
+ − 23
+ − 24 #if $pindelmax:
+ − 25 --p-indel-max=$pindelmax
+ − 26 #end if
+ − 27
+ − 28 #if $pmeanerror:
+ − 29 --p-mean-error=$pmeanerror
+ − 30 #end if
+ − 31
+ − 32 --o-representative-sequences=orepresentativesequences --o-table=otable --o-stats=ostats
+ − 33
+ − 34 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
+ − 35
+ − 36 #if str($pjobstostart):
+ − 37 --p-jobs-to-start="$pjobstostart"
+ − 38 #end if
+ − 39
+ − 40 #if $pminreads:
+ − 41 --p-min-reads=$pminreads
+ − 42 #end if
+ − 43
+ − 44 #if $pminsize:
+ − 45 --p-min-size=$pminsize
+ − 46 #end if
+ − 47
+ − 48 --p-sample-stats
+ − 49 ;
+ − 50 cp orepresentativesequences.qza $orepresentativesequences;
+ − 51 cp otable.qza $otable;
+ − 52 cp ostats.qza $ostats;
+ − 53 ]]></command>
+ − 54 <inputs>
+ − 55 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
+ − 56 <param format="qza,no_unzip.zip" label="--i-reference-seqs: FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data"/>
+ − 57 <param label="--p-trim-length: Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text"/>
+ − 58 <param label="--p-mean-error: The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
+ − 59 <param label="--p-indel-prob: Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
+ − 60 <param label="--p-indel-max: Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
+ − 61 <param label="--p-min-reads: Retain only features appearing at least min_reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
+ − 62 <param label="--p-min-size: In each sample, discard all features with an abundance less than min_size. [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
+ − 63 <param label="--p-hashed-feature-ids: --p-no-hashed-feature-ids If true, hash the feature IDs. [default: True]" name="phashedfeatureids" checked="True" type="boolean"/>
+ − 64 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 65 </inputs>
+ − 66 <outputs>
+ − 67 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
+ − 68 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
+ − 69 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
+ − 70 </outputs>
+ − 71 <help><![CDATA[
+ − 72 Deblur sequences using a user-specified positive filter.
+ − 73 ---------------------------------------------------------
+ − 74
+ − 75 Perform sequence quality control for Illumina data using the Deblur
+ − 76 workflow, including positive alignment-based filtering. Only forward reads
+ − 77 are supported at this time. This mode of execution is particularly useful
+ − 78 when operating on non-16S data. For example, to apply Deblur to 18S data,
+ − 79 you would want to specify a reference composed of 18S sequences in order to
+ − 80 filter out sequences which do not appear to be 18S. The assessment is
+ − 81 performed by local alignment using SortMeRNA with a permissive e-value
+ − 82 threshold.
+ − 83
+ − 84 Parameters
+ − 85 ----------
+ − 86 demultiplexed_seqs : SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality]
+ − 87 The demultiplexed sequences to be denoised.
+ − 88 reference_seqs : FeatureData[Sequence]
+ − 89 Positive filtering database. Keep all sequences aligning to these
+ − 90 sequences.
+ − 91 trim_length : Int
+ − 92 Sequence trim length, specify -1 to disable trimming.
+ − 93 sample_stats : Bool, optional
+ − 94 If true, gather stats per sample.
+ − 95 mean_error : Float, optional
+ − 96 The mean per nucleotide error, used for original sequence estimate.
+ − 97 indel_prob : Float, optional
+ − 98 Insertion/deletion (indel) probability (same for N indels).
+ − 99 indel_max : Int, optional
+ − 100 Maximum number of insertion/deletions.
+ − 101 min_reads : Int, optional
+ − 102 Retain only features appearing at least min_reads times across all
+ − 103 samples in the resulting feature table.
+ − 104 min_size : Int, optional
+ − 105 In each sample, discard all features with an abundance less than
+ − 106 min_size.
+ − 107 jobs_to_start : Int, optional
+ − 108 Number of jobs to start (if to run in parallel).
+ − 109 hashed_feature_ids : Bool, optional
+ − 110 If true, hash the feature IDs.
+ − 111
+ − 112 Returns
+ − 113 -------
+ − 114 table : FeatureTable[Frequency]
+ − 115 The resulting denoised feature table.
+ − 116 representative_sequences : FeatureData[Sequence]
+ − 117 The resulting feature sequences.
+ − 118 stats : DeblurStats
+ − 119 Per-sample stats if requested.
+ − 120 ]]>
+ − 121 </help>
+ − 122 </tool>
