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comparison qiime2/qiime_deblur_denoise-16S.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S" version="2019.7"> 2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S"
3 <description> - Deblur sequences using a 16S positive filter.</description> 3 version="2020.8">
4 <requirements> 4 <description>Deblur sequences using a 16S positive filter.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime deblur denoise-16S 9 qiime deblur denoise-16S
9 10
10 --i-demultiplexed-seqs=$idemultiplexedseqs 11 --i-demultiplexed-seqs=$idemultiplexedseqs
11 12
13 --p-trim-length=$ptrimlength
12 14
15 --p-left-trim-len=$plefttrimlen
13 16
14 #if str($ptrimlength): 17 #if $psamplestats:
15 --p-trim-length=$ptrimlength
16 #end if
17
18 #if str($plefttrimlen):
19 --p-left-trim-len=$plefttrimlen
20 #end if
21
22 #if str($psamplestats):
23 --p-sample-stats 18 --p-sample-stats
24 #end if 19 #end if
25 20
26 #if str($pmeanerror): 21 --p-mean-error=$pmeanerror
27 --p-mean-error=$pmeanerror
28 #end if
29 22
30 #if str($pindelprob): 23 --p-indel-prob=$pindelprob
31 --p-indel-prob=$pindelprob
32 #end if
33 24
34 #if str($pindelmax): 25 --p-indel-max=$pindelmax
35 --p-indel-max=$pindelmax
36 #end if
37 26
38 #if str($pminreads): 27 --p-min-reads=$pminreads
39 --p-min-reads=$pminreads
40 #end if
41 28
42 #if str($pminsize): 29 --p-min-size=$pminsize
43 --p-min-size=$pminsize
44 #end if
45 30
46 #set $pjobstostart = '${GALAXY_SLOTS:-4}' 31 --p-jobs-to-start=$pjobstostart
47 32
48 #if str($pjobstostart): 33 #if $pnohashedfeatureids:
49 --p-jobs-to-start="$pjobstostart"
50 #end if
51
52
53 #if str($pnohashedfeatureids):
54 --p-no-hashed-feature-ids 34 --p-no-hashed-feature-ids
55 #end if 35 #end if
56 36
57 --o-table=otable 37 --o-table=otable
38
58 --o-representative-sequences=orepresentativesequences 39 --o-representative-sequences=orepresentativesequences
40
59 --o-stats=ostats 41 --o-stats=ostats
42
43 #if str($examples) != 'None':
44 --examples=$examples
45 #end if
46
60 ; 47 ;
61 cp otable.qza $otable;
62 cp orepresentativesequences.qza $orepresentativesequences;
63 cp ostats.qza $ostats 48 cp ostats.qza $ostats
64 ]]></command> 49
65 <inputs> 50 ]]></command>
66 <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"/> 51 <inputs>
67 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" value="" type="integer"/> 52 <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" />
68 <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"/> 53 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text" />
69 <param label="--p-sample-stats: --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean"/> 54 <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" />
70 <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"/> 55 <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" />
71 <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"/> 56 <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" />
72 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/> 57 <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" />
73 <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"/> 58 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
74 <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"/> 59 <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" />
75 <param label="--p-no-hashed-feature-ids: If false, hash the feature IDs. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/> 60 <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" />
76 </inputs> 61 <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs. [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
77 <outputs> 62 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
78 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/> 63
79 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/> 64 </inputs>
80 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/> 65
81 </outputs> 66 <outputs>
82 <help><![CDATA[ 67 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
68 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
69 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
70
71 </outputs>
72
73 <help><![CDATA[
83 Deblur sequences using a 16S positive filter. 74 Deblur sequences using a 16S positive filter.
84 ############################################# 75 ###############################################################
85 76
86 Perform sequence quality control for Illumina data using the Deblur 77 Perform sequence quality control for Illumina data using the Deblur
87 workflow with a 16S reference as a positive filter. Only forward reads are 78 workflow with a 16S reference as a positive filter. Only forward reads are
88 supported at this time. The specific reference used is the 88% OTUs from 79 supported at this time. The specific reference used is the 88% OTUs from
89 Greengenes 13_8. This mode of operation should only be used when data were 80 Greengenes 13_8. This mode of operation should only be used when data were
112 Retain only features appearing at least min_reads times across all 103 Retain only features appearing at least min_reads times across all
113 samples in the resulting feature table. 104 samples in the resulting feature table.
114 min_size : Int, optional 105 min_size : Int, optional
115 In each sample, discard all features with an abundance less than 106 In each sample, discard all features with an abundance less than
116 min_size. 107 min_size.
108 jobs_to_start : Int, optional
109 Number of jobs to start (if to run in parallel).
117 hashed_feature_ids : Bool, optional 110 hashed_feature_ids : Bool, optional
118 If true, hash the feature IDs. 111 If true, hash the feature IDs.
119 112
120 Returns 113 Returns
121 ------- 114 -------
123 The resulting denoised feature table. 116 The resulting denoised feature table.
124 representative_sequences : FeatureData[Sequence] 117 representative_sequences : FeatureData[Sequence]
125 The resulting feature sequences. 118 The resulting feature sequences.
126 stats : DeblurStats 119 stats : DeblurStats
127 Per-sample stats if requested. 120 Per-sample stats if requested.
128 ]]></help> 121 ]]></help>
129 <macros> 122 <macros>
130 <import>qiime_citation.xml</import> 123 <import>qiime_citation.xml</import>
131 </macros> 124 </macros>
132 <expand macro="qiime_citation"/> 125 <expand macro="qiime_citation"/>
133 </tool> 126 </tool>