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comparison qiime_deblur_denoise-16S.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S" version="2018.4">
3 <description>- Deblur sequences using a 16S positive filter.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime deblur denoise-16S --p-trim-length="$ptrimlength" --i-demultiplexed-seqs=$idemultiplexedseqs --o-representative-sequences=orepresentativesequences
9
10 #if $pmeanerror:
11 --p-mean-error=$pmeanerror
12 #end if
13
14 #if str($cmdconfig) != 'None':
15 --cmd-config=$cmdconfig
16 #end if
17
18 #if $pminreads:
19 --p-min-reads=$pminreads
20 #end if
21
22 #if $pindelprob:
23 --p-indel-prob=$pindelprob
24 #end if
25
26 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
27
28 #if str($pjobstostart):
29 --p-jobs-to-start="$pjobstostart"
30 #end if
31
32 --o-stats=ostats
33
34 #if $pindelmax:
35 --p-indel-max=$pindelmax
36 #end if
37
38 #if $pminsize:
39 --p-min-size=$pminsize
40 #end if
41
42 #if $phashedfeatureids:
43 --p-hashed-feature-ids
44 #else
45 --p-no-hashed-feature-ids
46 #end if
47
48 --o-table=otable
49
50 --p-sample-stats
51
52 ;
53 cp orepresentativesequences.qza $orepresentativesequences;
54 cp ostats.qza $ostats;
55 cp otable.qza $otable;
56 ]]></command>
57 <inputs>
58 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
59 <param label="--p-trim-length: Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text"/>
60 <param label="--p-mean-error: The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
61 <param label="--p-indel-prob: Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
62 <param label="--p-indel-max: Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
63 <param label="--p-min-reads: Retain only features appearing at least min_reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
64 <param label="--p-min-size: In each sample, discard all features with an abundance less than min_size. [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
65 <param label="--p-hashed-feature-ids: --p-no-hashed-feature-ids If true, hash the feature IDs. [default: True]" name="phashedfeatureids" checked="True" type="boolean"/>
66 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
67 </inputs>
68 <outputs>
69 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
70 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
71 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
72 </outputs>
73 <help><![CDATA[
74 Deblur sequences using a 16S positive filter.
75 ----------------------------------------------
76
77 Perform sequence quality control for Illumina data using the Deblur
78 workflow with a 16S reference as a positive filter. Only forward reads are
79 supported at this time. The specific reference used is the 88% OTUs from
80 Greengenes 13_8. This mode of operation should only be used when data were
81 generated from a 16S amplicon protocol on an Illumina platform. The
82 reference is only used to assess whether each sequence is likely to be 16S
83 by a local alignment using SortMeRNA with a permissive e-value; the
84 reference is not used to characterize the sequences.
85
86 Parameters
87 ----------
88 demultiplexed_seqs : SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality]
89 The demultiplexed sequences to be denoised.
90 trim_length : Int
91 Sequence trim length, specify -1 to disable trimming.
92 sample_stats : Bool, optional
93 If true, gather stats per sample.
94 mean_error : Float, optional
95 The mean per nucleotide error, used for original sequence estimate.
96 indel_prob : Float, optional
97 Insertion/deletion (indel) probability (same for N indels).
98 indel_max : Int, optional
99 Maximum number of insertion/deletions.
100 min_reads : Int, optional
101 Retain only features appearing at least min_reads times across all
102 samples in the resulting feature table.
103 min_size : Int, optional
104 In each sample, discard all features with an abundance less than
105 min_size.
106 jobs_to_start : Int, optional
107 Number of jobs to start (if to run in parallel).
108 hashed_feature_ids : Bool, optional
109 If true, hash the feature IDs.
110
111 Returns
112 -------
113 table : FeatureTable[Frequency]
114 The resulting denoised feature table.
115 representative_sequences : FeatureData[Sequence]
116 The resulting feature sequences.
117 stats : DeblurStats
118 Per-sample stats if requested.
119 ]]>
120 </help>
121 </tool>