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comparison qiime2/qiime_vsearch_join-pairs.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.4">
3 <description> - Join paired-end reads.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime vsearch join-pairs
9
10 --i-demultiplexed-seqs=$idemultiplexedseqs
11
12 #if str($ptruncqual):
13 --p-truncqual="$ptruncqual"
14 #end if
15
16 #if $pminlen:
17 --p-minlen=$pminlen
18 #end if
19
20 #if str($pmaxns):
21 --p-maxns="$pmaxns"
22 #end if
23
24 #if $pallowmergestagger:
25 --p-allowmergestagger
26 #end if
27
28 #if $pminovlen:
29 --p-minovlen=$pminovlen
30 #end if
31
32 #if $pmaxdiffs:
33 --p-maxdiffs=$pmaxdiffs
34 #end if
35
36 #if str($pminmergelen):
37 --p-minmergelen="$pminmergelen"
38 #end if
39
40 #if str($pmaxmergelen):
41 --p-maxmergelen="$pmaxmergelen"
42 #end if
43
44 #if str($pmaxee):
45 --p-maxee="$pmaxee"
46 #end if
47
48 #if $pqmin:
49 --p-qmin=$pqmin
50 #end if
51
52 #if $pqminout:
53 --p-qminout=$pqminout
54 #end if
55
56 #if $pqmax:
57 --p-qmax=$pqmax
58 #end if
59
60 #if $pqmaxout:
61 --p-qmaxout=$pqmaxout
62 #end if
63
64 --o-joined-sequences=ojoinedsequences
65 ;
66 cp ojoinedsequences.qza $ojoinedsequences
67 ]]></command>
68 <inputs>
69 <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"/>
70 <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="True" min="0" type="integer"/>
71 <param label="--p-minlen: INTEGER Sequences shorter than minlen after truncation are Range(0, None) discarded. [default: 1]" name="pminlen" optional="True" type="integer" min="0" value="1"/>
72 <param label="--p-maxns: INTEGER Sequences with more than maxns N characters are Range(0, None) discarded. [optional]" name="pmaxns" optional="True" min="0" type="integer"/>
73 <param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean"/>
74 <param label="--p-minovlen: INTEGER Minimum overlap length of forward and reverse reads Range(0, None) for joining. [default: 10]" name="pminovlen" optional="True" type="integer" min="0" value="10"/>
75 <param label="--p-maxdiffs: INTEGER Maximum number of mismatches in the forward/reverse Range(0, None) read overlap for joining. [default: 10]" name="pmaxdiffs" optional="True" type="integer" min="0" value="10"/>
76 <param label="--p-minmergelen: INTEGER Range(0, None) Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="True" min="0" type="integer"/>
77 <param label="--p-maxmergelen: INTEGER Range(0, None) Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="True" min="0" type="integer"/>
78 <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="True" min="0" type="float"/>
79 <param label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" name="pqmin" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
80 <param label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" name="pqminout" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
81 <param label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" name="pqmax" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
82 <param label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" name="pqmaxout" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
83 </inputs>
84 <outputs>
85 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences"/>
86 </outputs>
87 <help><![CDATA[
88 Join paired-end reads.
89 ######################
90
91 Join paired-end sequence reads using vsearch's merge_pairs function. The
92 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
93 when working with older fastq sequence data. See the vsearch documentation
94 for details on how paired-end joining is performed, and for more
95 information on the parameters to this method.
96
97 Parameters
98 ----------
99 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
100 The demultiplexed paired-end sequences to be joined.
101 truncqual : Int % Range(0, None), optional
102 Truncate sequences at the first base with the specified quality score
103 value or lower.
104 minlen : Int % Range(0, None), optional
105 Sequences shorter than minlen after truncation are discarded.
106 maxns : Int % Range(0, None), optional
107 Sequences with more than maxns N characters are discarded.
108 allowmergestagger : Bool, optional
109 Allow joining of staggered read pairs.
110 minovlen : Int % Range(0, None), optional
111 Minimum overlap length of forward and reverse reads for joining.
112 maxdiffs : Int % Range(0, None), optional
113 Maximum number of mismatches in the forward/reverse read overlap for
114 joining.
115 minmergelen : Int % Range(0, None), optional
116 Minimum length of the joined read to be retained.
117 maxmergelen : Int % Range(0, None), optional
118 Maximum length of the joined read to be retained.
119 maxee : Float % Range(0.0, None), optional
120 Maximum number of expected errors in the joined read to be retained.
121 qmin : Int % Range(-5, 2, inclusive_end=True), optional
122 The minimum allowed quality score in the input.
123 qminout : Int % Range(-5, 2, inclusive_end=True), optional
124 The minimum allowed quality score to use in output.
125 qmax : Int % Range(40, 41, inclusive_end=True), optional
126 The maximum allowed quality score in the input.
127 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
128 The maximum allowed quality score to use in output.
129
130 Returns
131 -------
132 joined_sequences : SampleData[JoinedSequencesWithQuality]
133 The joined sequences.
134 ]]></help>
135 <macros>
136 <import>qiime_citation.xml</import>
137 </macros>
138 <expand macro="qiime_citation"/>
139 </tool>