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comparison qiime2/qiime_deblur_denoise-16S.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children de4c22a52df4
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S" version="2019.4">
3 <description> - Deblur sequences using a 16S positive filter.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime deblur denoise-16S
9
10 --i-demultiplexed-seqs=$idemultiplexedseqs
11 --p-trim-length="$ptrimlength"
12
13 #if $plefttrimlen:
14 --p-left-trim-len=$plefttrimlen
15 #end if
16
17 #if $psamplestats:
18 --p-sample-stats
19 #end if
20
21 #if $pmeanerror:
22 --p-mean-error=$pmeanerror
23 #end if
24
25 #if $pindelprob:
26 --p-indel-prob=$pindelprob
27 #end if
28
29 #if $pindelmax:
30 --p-indel-max=$pindelmax
31 #end if
32
33 #if $pminreads:
34 --p-min-reads=$pminreads
35 #end if
36
37 #if $pminsize:
38 --p-min-size=$pminsize
39 #end if
40
41 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
42
43 #if str($pjobstostart):
44 --p-jobs-to-start="$pjobstostart"
45 #end if
46
47
48 #if $pnohashedfeatureids:
49 --p-no-hashed-feature-ids
50 #end if
51
52 --o-table=otable
53 --o-representative-sequences=orepresentativesequences
54 --o-stats=ostats
55 ;
56 cp otable.qza $otable;
57 cp orepresentativesequences.qza $orepresentativesequences;
58 cp ostats.qza $ostats
59 ]]></command>
60 <inputs>
61 <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"/>
62 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" value="" type="integer"/>
63 <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]" name="plefttrimlen" optional="True" type="integer" min="0" value="0"/>
64 <param label="--p-sample-stats: --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean"/>
65 <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"/>
66 <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"/>
67 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
68 <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"/>
69 <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"/>
70 <param label="--p-no-hashed-feature-ids: If false, hash the feature IDs. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
71 </inputs>
72 <outputs>
73 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
74 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
75 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
76 </outputs>
77 <help><![CDATA[
78 Deblur sequences using a 16S positive filter.
79 #############################################
80
81 Perform sequence quality control for Illumina data using the Deblur
82 workflow with a 16S reference as a positive filter. Only forward reads are
83 supported at this time. The specific reference used is the 88% OTUs from
84 Greengenes 13_8. This mode of operation should only be used when data were
85 generated from a 16S amplicon protocol on an Illumina platform. The
86 reference is only used to assess whether each sequence is likely to be 16S
87 by a local alignment using SortMeRNA with a permissive e-value; the
88 reference is not used to characterize the sequences.
89
90 Parameters
91 ----------
92 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
93 The demultiplexed sequences to be denoised.
94 trim_length : Int
95 Sequence trim length, specify -1 to disable trimming.
96 left_trim_len : Int % Range(0, None), optional
97 Sequence trimming from the 5' end. A value of 0 will disable this trim.
98 sample_stats : Bool, optional
99 If true, gather stats per sample.
100 mean_error : Float, optional
101 The mean per nucleotide error, used for original sequence estimate.
102 indel_prob : Float, optional
103 Insertion/deletion (indel) probability (same for N indels).
104 indel_max : Int, optional
105 Maximum number of insertion/deletions.
106 min_reads : Int, optional
107 Retain only features appearing at least min_reads times across all
108 samples in the resulting feature table.
109 min_size : Int, optional
110 In each sample, discard all features with an abundance less than
111 min_size.
112 hashed_feature_ids : Bool, optional
113 If true, hash the feature IDs.
114
115 Returns
116 -------
117 table : FeatureTable[Frequency]
118 The resulting denoised feature table.
119 representative_sequences : FeatureData[Sequence]
120 The resulting feature sequences.
121 stats : DeblurStats
122 Per-sample stats if requested.
123 ]]></help>
124 <macros>
125 <import>qiime_citation.xml</import>
126 </macros>
127 <expand macro="qiime_citation"/>
128 </tool>