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