Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_deblur_denoise-other.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" | |
3 version="2020.8"> | |
4 <description>Deblur sequences using a user-specified positive filter.</description> | |
5 <requirements> | |
6 <requirement type="package" version="2020.8">qiime2</requirement> | |
7 </requirements> | |
8 <command><![CDATA[ | |
9 qiime deblur denoise-other | |
10 | |
11 --i-demultiplexed-seqs=$idemultiplexedseqs | |
12 | |
13 --i-reference-seqs=$ireferenceseqs | |
14 | |
15 --p-trim-length=$ptrimlength | |
16 | |
17 --p-left-trim-len=$plefttrimlen | |
18 | |
19 #if $psamplestats: | |
20 --p-sample-stats | |
21 #end if | |
22 | |
23 --p-mean-error=$pmeanerror | |
24 | |
25 --p-indel-prob=$pindelprob | |
26 | |
27 --p-indel-max=$pindelmax | |
28 | |
29 --p-min-reads=$pminreads | |
30 | |
31 --p-min-size=$pminsize | |
32 | |
33 --p-jobs-to-start=$pjobstostart | |
34 | |
35 #if $pnohashedfeatureids: | |
36 --p-no-hashed-feature-ids | |
37 #end if | |
38 | |
39 --o-table=otable | |
40 | |
41 --o-representative-sequences=orepresentativesequences | |
42 | |
43 --o-stats=ostats | |
44 | |
45 #if str($examples) != 'None': | |
46 --examples=$examples | |
47 #end if | |
48 | |
49 ; | |
50 cp ostats.qza $ostats | |
51 | |
52 ]]></command> | |
53 <inputs> | |
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" /> | |
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" /> | |
56 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text" /> | |
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" /> | |
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" /> | |
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" /> | |
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" /> | |
61 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3" /> | |
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" /> | |
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" /> | |
64 <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs. [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" /> | |
65 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
66 | |
67 </inputs> | |
68 | |
69 <outputs> | |
70 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" /> | |
71 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" /> | |
72 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" /> | |
73 | |
74 </outputs> | |
75 | |
76 <help><![CDATA[ | |
77 Deblur sequences using a user-specified positive filter. | |
78 ############################################################### | |
79 | |
80 Perform sequence quality control for Illumina data using the Deblur | |
81 workflow, including positive alignment-based filtering. Only forward reads | |
82 are supported at this time. This mode of execution is particularly useful | |
83 when operating on non-16S data. For example, to apply Deblur to 18S data, | |
84 you would want to specify a reference composed of 18S sequences in order to | |
85 filter out sequences which do not appear to be 18S. The assessment is | |
86 performed by local alignment using SortMeRNA with a permissive e-value | |
87 threshold. | |
88 | |
89 Parameters | |
90 ---------- | |
91 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] | |
92 The demultiplexed sequences to be denoised. | |
93 reference_seqs : FeatureData[Sequence] | |
94 Positive filtering database. Keep all sequences aligning to these | |
95 sequences. | |
96 trim_length : Int | |
97 Sequence trim length, specify -1 to disable trimming. | |
98 left_trim_len : Int % Range(0, None), optional | |
99 Sequence trimming from the 5' end. A value of 0 will disable this trim. | |
100 sample_stats : Bool, optional | |
101 If true, gather stats per sample. | |
102 mean_error : Float, optional | |
103 The mean per nucleotide error, used for original sequence estimate. | |
104 indel_prob : Float, optional | |
105 Insertion/deletion (indel) probability (same for N indels). | |
106 indel_max : Int, optional | |
107 Maximum number of insertion/deletions. | |
108 min_reads : Int, optional | |
109 Retain only features appearing at least min_reads times across all | |
110 samples in the resulting feature table. | |
111 min_size : Int, optional | |
112 In each sample, discard all features with an abundance less than | |
113 min_size. | |
114 jobs_to_start : Int, optional | |
115 Number of jobs to start (if to run in parallel). | |
116 hashed_feature_ids : Bool, optional | |
117 If true, hash the feature IDs. | |
118 | |
119 Returns | |
120 ------- | |
121 table : FeatureTable[Frequency] | |
122 The resulting denoised feature table. | |
123 representative_sequences : FeatureData[Sequence] | |
124 The resulting feature sequences. | |
125 stats : DeblurStats | |
126 Per-sample stats if requested. | |
127 ]]></help> | |
128 <macros> | |
129 <import>qiime_citation.xml</import> | |
130 </macros> | |
131 <expand macro="qiime_citation"/> | |
132 </tool> |