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1 <?xml version="1.0" ?>
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2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other"
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3 version="2020.8">
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4 <description>Deblur sequences using a user-specified positive filter.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime deblur denoise-other
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10
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11 --i-demultiplexed-seqs=$idemultiplexedseqs
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12
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13 --i-reference-seqs=$ireferenceseqs
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14
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15 --p-trim-length=$ptrimlength
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16
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17 --p-left-trim-len=$plefttrimlen
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18
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19 #if $psamplestats:
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20 --p-sample-stats
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21 #end if
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22
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23 --p-mean-error=$pmeanerror
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24
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25 --p-indel-prob=$pindelprob
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26
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27 --p-indel-max=$pindelmax
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28
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29 --p-min-reads=$pminreads
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30
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31 --p-min-size=$pminsize
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32
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33 --p-jobs-to-start=$pjobstostart
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34
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35 #if $pnohashedfeatureids:
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36 --p-no-hashed-feature-ids
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37 #end if
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38
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39 --o-table=otable
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40
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41 --o-representative-sequences=orepresentativesequences
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42
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43 --o-stats=ostats
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44
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45 #if str($examples) != 'None':
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46 --examples=$examples
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47 #end if
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48
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49 ;
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50 cp ostats.qza $ostats
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51
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52 ]]></command>
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53 <inputs>
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54 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
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55 <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data" />
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56 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text" />
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57 <param label="--p-left-trim-len: INTEGER Range(0, None) Sequence trimming from the 5\' end. A value of 0 will disable this trim. [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
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58 <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean" />
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59 <param label="--p-mean-error: NUMBER The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005" />
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60 <param label="--p-indel-prob: NUMBER Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01" />
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61 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
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62 <param label="--p-min-reads: INTEGER 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" />
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63 <param label="--p-min-size: INTEGER In each sample, discard all features with an abundance less than min-size. [default: 2]" name="pminsize" optional="True" type="integer" value="2" />
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64 <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs. [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
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65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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66
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67 </inputs>
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68
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69 <outputs>
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70 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
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71 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
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72 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
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73
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74 </outputs>
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75
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76 <help><![CDATA[
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77 Deblur sequences using a user-specified positive filter.
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78 ###############################################################
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79
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80 Perform sequence quality control for Illumina data using the Deblur
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81 workflow, including positive alignment-based filtering. Only forward reads
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82 are supported at this time. This mode of execution is particularly useful
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83 when operating on non-16S data. For example, to apply Deblur to 18S data,
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84 you would want to specify a reference composed of 18S sequences in order to
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85 filter out sequences which do not appear to be 18S. The assessment is
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86 performed by local alignment using SortMeRNA with a permissive e-value
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87 threshold.
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88
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89 Parameters
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90 ----------
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91 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
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92 The demultiplexed sequences to be denoised.
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93 reference_seqs : FeatureData[Sequence]
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94 Positive filtering database. Keep all sequences aligning to these
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95 sequences.
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96 trim_length : Int
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97 Sequence trim length, specify -1 to disable trimming.
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98 left_trim_len : Int % Range(0, None), optional
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99 Sequence trimming from the 5' end. A value of 0 will disable this trim.
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100 sample_stats : Bool, optional
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101 If true, gather stats per sample.
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102 mean_error : Float, optional
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103 The mean per nucleotide error, used for original sequence estimate.
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104 indel_prob : Float, optional
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105 Insertion/deletion (indel) probability (same for N indels).
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106 indel_max : Int, optional
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107 Maximum number of insertion/deletions.
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108 min_reads : Int, optional
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109 Retain only features appearing at least min_reads times across all
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110 samples in the resulting feature table.
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111 min_size : Int, optional
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112 In each sample, discard all features with an abundance less than
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113 min_size.
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114 jobs_to_start : Int, optional
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115 Number of jobs to start (if to run in parallel).
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116 hashed_feature_ids : Bool, optional
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117 If true, hash the feature IDs.
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118
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119 Returns
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120 -------
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121 table : FeatureTable[Frequency]
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122 The resulting denoised feature table.
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123 representative_sequences : FeatureData[Sequence]
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124 The resulting feature sequences.
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125 stats : DeblurStats
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126 Per-sample stats if requested.
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127 ]]></help>
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128 <macros>
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129 <import>qiime_citation.xml</import>
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130 </macros>
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131 <expand macro="qiime_citation"/>
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132 </tool> |
