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