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comparison qiime2/qiime_vsearch_join-pairs.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs"
3 version="2020.8">
4 <description>Join paired-end reads.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime vsearch join-pairs
10
11 --i-demultiplexed-seqs=$idemultiplexedseqs
12
13 #if str($ptruncqual):
14 --p-truncqual=$ptruncqual
15 #end if
16 --p-minlen=$pminlen
17
18 #if str($pmaxns):
19 --p-maxns=$pmaxns
20 #end if
21 #if $pallowmergestagger:
22 --p-allowmergestagger
23 #end if
24
25 --p-minovlen=$pminovlen
26
27 --p-maxdiffs=$pmaxdiffs
28
29 #if str($pminmergelen):
30 --p-minmergelen=$pminmergelen
31 #end if
32 #if str($pmaxmergelen):
33 --p-maxmergelen=$pmaxmergelen
34 #end if
35 #if str($pmaxee):
36 --p-maxee=$pmaxee
37 #end if
38 --p-qmin=$pqmin
39
40 --p-qminout=$pqminout
41
42 --p-qmax=$pqmax
43
44 --p-qmaxout=$pqmaxout
45
46 --p-threads=$pthreads
47
48 --o-joined-sequences=ojoinedsequences
49
50 #if str($examples) != 'None':
51 --examples=$examples
52 #end if
53
54 ;
55 cp ojoinedsequences.qza $ojoinedsequences
56
57 ]]></command>
58 <inputs>
59 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data" />
60 <param label="--p-truncqual: INTEGER Truncate sequences at the first base with the Range(0, None) specified quality score value or lower. [optional]" name="ptruncqual" optional="False" type="text" />
61 <param label="--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]" min="0" name="pminlen" optional="True" type="integer" value="1" />
62 <param label="--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]" name="pmaxns" optional="False" type="text" />
63 <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" />
64 <param label="--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]" min="0" name="pminovlen" optional="True" type="integer" value="10" />
65 <param label="--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]" min="0" name="pmaxdiffs" optional="True" type="integer" value="10" />
66 <param label="--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="False" type="text" />
67 <param label="--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="False" type="text" />
68 <param label="--p-maxee: NUMBER Maximum number of expected errors in the joined read Range(0.0, None) to be retained. [optional]" name="pmaxee" optional="False" type="text" />
69 <param exclude_max="False" label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" max="2" min="-5" name="pqmin" optional="True" type="integer" value="0" />
70 <param exclude_max="False" label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" max="2" min="-5" name="pqminout" optional="True" type="integer" value="0" />
71 <param exclude_max="False" label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" max="41" min="40" name="pqmax" optional="True" type="integer" value="41" />
72 <param exclude_max="False" label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" max="41" min="40" name="pqmaxout" optional="True" type="integer" value="41" />
73 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
74
75 </inputs>
76
77 <outputs>
78 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences" />
79
80 </outputs>
81
82 <help><![CDATA[
83 Join paired-end reads.
84 ###############################################################
85
86 Join paired-end sequence reads using vsearch's merge_pairs function. The
87 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
88 when working with older fastq sequence data. See the vsearch documentation
89 for details on how paired-end joining is performed, and for more
90 information on the parameters to this method.
91
92 Parameters
93 ----------
94 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
95 The demultiplexed paired-end sequences to be joined.
96 truncqual : Int % Range(0, None), optional
97 Truncate sequences at the first base with the specified quality score
98 value or lower.
99 minlen : Int % Range(0, None), optional
100 Sequences shorter than minlen after truncation are discarded.
101 maxns : Int % Range(0, None), optional
102 Sequences with more than maxns N characters are discarded.
103 allowmergestagger : Bool, optional
104 Allow joining of staggered read pairs.
105 minovlen : Int % Range(0, None), optional
106 Minimum overlap length of forward and reverse reads for joining.
107 maxdiffs : Int % Range(0, None), optional
108 Maximum number of mismatches in the forward/reverse read overlap for
109 joining.
110 minmergelen : Int % Range(0, None), optional
111 Minimum length of the joined read to be retained.
112 maxmergelen : Int % Range(0, None), optional
113 Maximum length of the joined read to be retained.
114 maxee : Float % Range(0.0, None), optional
115 Maximum number of expected errors in the joined read to be retained.
116 qmin : Int % Range(-5, 2, inclusive_end=True), optional
117 The minimum allowed quality score in the input.
118 qminout : Int % Range(-5, 2, inclusive_end=True), optional
119 The minimum allowed quality score to use in output.
120 qmax : Int % Range(40, 41, inclusive_end=True), optional
121 The maximum allowed quality score in the input.
122 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
123 The maximum allowed quality score to use in output.
124 threads : Int % Range(0, 8, inclusive_end=True), optional
125 The number of threads to use for computation. Does not scale much past
126 4 threads.
127
128 Returns
129 -------
130 joined_sequences : SampleData[JoinedSequencesWithQuality]
131 The joined sequences.
132 ]]></help>
133 <macros>
134 <import>qiime_citation.xml</import>
135 </macros>
136 <expand macro="qiime_citation"/>
137 </tool>