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comparison qiime2/qiime_deblur_denoise-other.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2018.4">
3 <description> - Deblur sequences using a user-specified positive filter.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime deblur denoise-other --i-demultiplexed-seqs=$idemultiplexedseqs --p-trim-length="$ptrimlength" --i-reference-seqs=$ireferenceseqs
9
10 #if str($cmdconfig) != 'None':
11 --cmd-config=$cmdconfig
12 #end if
13
14 #if $phashedfeatureids:
15 --p-hashed-feature-ids
16 #else
17 --p-no-hashed-feature-ids
18 #end if
19
20 #if $pindelprob:
21 --p-indel-prob=$pindelprob
22 #end if
23
24 #if $pindelmax:
25 --p-indel-max=$pindelmax
26 #end if
27
28 #if $pmeanerror:
29 --p-mean-error=$pmeanerror
30 #end if
31
32 --o-representative-sequences=orepresentativesequences --o-table=otable --o-stats=ostats
33
34 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
35
36 #if str($pjobstostart):
37 --p-jobs-to-start="$pjobstostart"
38 #end if
39
40 #if $pminreads:
41 --p-min-reads=$pminreads
42 #end if
43
44 #if $pminsize:
45 --p-min-size=$pminsize
46 #end if
47
48 --p-sample-stats
49 ;
50 cp orepresentativesequences.qza $orepresentativesequences;
51 cp otable.qza $otable;
52 cp ostats.qza $ostats;
53 ]]></command>
54 <inputs>
55 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
56 <param format="qza,no_unzip.zip" label="--i-reference-seqs: FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data"/>
57 <param label="--p-trim-length: Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text"/>
58 <param label="--p-mean-error: The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
59 <param label="--p-indel-prob: Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
60 <param label="--p-indel-max: Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
61 <param label="--p-min-reads: Retain only features appearing at least min_reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
62 <param label="--p-min-size: In each sample, discard all features with an abundance less than min_size. [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
63 <param label="--p-hashed-feature-ids: --p-no-hashed-feature-ids If true, hash the feature IDs. [default: True]" name="phashedfeatureids" checked="True" type="boolean"/>
64 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
65 </inputs>
66 <outputs>
67 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
68 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
69 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
70 </outputs>
71 <help><![CDATA[
72 Deblur sequences using a user-specified positive filter.
73 ---------------------------------------------------------
74
75 Perform sequence quality control for Illumina data using the Deblur
76 workflow, including positive alignment-based filtering. Only forward reads
77 are supported at this time. This mode of execution is particularly useful
78 when operating on non-16S data. For example, to apply Deblur to 18S data,
79 you would want to specify a reference composed of 18S sequences in order to
80 filter out sequences which do not appear to be 18S. The assessment is
81 performed by local alignment using SortMeRNA with a permissive e-value
82 threshold.
83
84 Parameters
85 ----------
86 demultiplexed_seqs : SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality]
87 The demultiplexed sequences to be denoised.
88 reference_seqs : FeatureData[Sequence]
89 Positive filtering database. Keep all sequences aligning to these
90 sequences.
91 trim_length : Int
92 Sequence trim length, specify -1 to disable trimming.
93 sample_stats : Bool, optional
94 If true, gather stats per sample.
95 mean_error : Float, optional
96 The mean per nucleotide error, used for original sequence estimate.
97 indel_prob : Float, optional
98 Insertion/deletion (indel) probability (same for N indels).
99 indel_max : Int, optional
100 Maximum number of insertion/deletions.
101 min_reads : Int, optional
102 Retain only features appearing at least min_reads times across all
103 samples in the resulting feature table.
104 min_size : Int, optional
105 In each sample, discard all features with an abundance less than
106 min_size.
107 jobs_to_start : Int, optional
108 Number of jobs to start (if to run in parallel).
109 hashed_feature_ids : Bool, optional
110 If true, hash the feature IDs.
111
112 Returns
113 -------
114 table : FeatureTable[Frequency]
115 The resulting denoised feature table.
116 representative_sequences : FeatureData[Sequence]
117 The resulting feature sequences.
118 stats : DeblurStats
119 Per-sample stats if requested.
120 ]]>
121 </help>
122 <macros>
123 <import>qiime_citation.xml</import>
124 </macros>
125 <expand macro="qiime_citation" />
126 </tool>