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comparison qiime_vsearch_join-pairs.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2018.4">
3 <description> - Join paired-end reads.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime vsearch join-pairs --i-demultiplexed-seqs=$idemultiplexedseqs
10
11 #if $pminovlen:
12 --p-minovlen=$pminovlen
13 #end if
14
15 #if str($ptruncqual):
16 --p-truncqual="$ptruncqual"
17 #end if
18
19 #if str($cmdconfig) != 'None':
20 --cmd-config=$cmdconfig
21 #end if
22
23 #if str($pminmergelen):
24 --p-minmergelen="$pminmergelen"
25 #end if
26
27 #if $pmaxdiffs:
28 --p-maxdiffs=$pmaxdiffs
29 #end if
30
31 #if str($pqminout):
32 --p-qminout="$pqminout"
33 #end if
34
35 #if str($pmaxmergelen):
36 --p-maxmergelen="$pmaxmergelen"
37 #end if
38
39 #if str($pmaxns):
40 --p-maxns="$pmaxns"
41 #end if
42
43 #if $pallowmergestagger:
44 --p-allowmergestagger
45 #else
46 --p-no-allowmergestagger
47 #end if
48
49 #if $pminlen:
50 --p-minlen=$pminlen
51 #end if
52
53 #if $pqmax:
54 --p-qmax=$pqmax
55 #end if
56
57 #if str($pmaxee):
58 --p-maxee="$pmaxee"
59 #end if
60
61 #if str($pqmin):
62 --p-qmin="$pqmin"
63 #end if
64
65 #if $pqmaxout:
66 --p-qmaxout=$pqmaxout
67 #end if
68 --o-joined-sequences=ojoinedsequences;
69
70 cp ojoinedsequences.qza $ojoinedsequences;
71 ]]>
72 </command>
73 <inputs>
74 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
75
76 <param label="--p-truncqual: Truncate sequences at the first base with the specified quality score value or lower. [optional]" name="ptruncqual" optional="True" type="text"/>
77
78 <param label="--p-minlen: Sequences shorter than minlen after truncation are discarded. [default: 1]" name="pminlen" optional="True" type="integer" value="1"/>
79 <param label="--p-maxns: Sequences with more than maxns N characters are discarded. [optional]" name="pmaxns" optional="True" type="text"/>
80
81 <param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" checked="False" type="boolean"/>
82
83 <param label="--p-minovlen: Minimum overlap length of forward and reverse reads for joining. [default: 10]" name="pminovlen" optional="True" type="integer" value="10"/>
84 <param label="--p-maxdiffs: Maximum number of mismatches in the forward/reverse read overlap for joining. [default: 10]" name="pmaxdiffs" optional="True" type="integer" value="10"/>
85
86 <param label="--p-minmergelen: Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="True" type="text"/>
87 <param label="--p-maxmergelen: Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="True" type="text"/>
88
89 <param label="--p-maxee: Maximum number of expected errors in the joined read to be retained. [optional]" name="pmaxee" optional="True" type="text"/>
90
91 <param label="--p-qmin: The minimum allowed quality score in the input. [default: 0]" name="pqmin" optional="True" type="text" value="0"/>
92 <param label="--p-qminout: The minimum allowed quality score to use in output. [default: 0]" name="pqminout" optional="True" type="text" value="0"/>
93
94 <param label="--p-qmax: The maximum allowed quality score in the input. [default: 41]" name="pqmax" optional="True" type="integer" value="41"/>
95 <param label="--p-qmaxout: The maximum allowed quality score to use in output. [default: 41]" name="pqmaxout" optional="True" type="integer" value="41"/>
96
97 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
98 </inputs>
99 <outputs>
100 <data format="qza" label="${tool.name} on ${on_string}: joined-sequences.qza" name="ojoinedsequences"/>
101 </outputs>
102 <help>
103 <![CDATA[
104 Join paired-end reads.
105 -----------------------
106
107 Join paired-end sequence reads using vsearch's merge_pairs function. The
108 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
109 when working with older fastq sequence data. See the vsearch documentation
110 for details on how paired-end joining is performed, and for more
111 information on the parameters to this method.
112
113 Parameters
114 ----------
115 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
116 The demultiplexed paired-end sequences to be joined.
117 truncqual : Int % Range(0, None), optional
118 Truncate sequences at the first base with the specified quality score
119 value or lower.
120 minlen : Int % Range(0, None), optional
121 Sequences shorter than minlen after truncation are discarded.
122 maxns : Int % Range(0, None), optional
123 Sequences with more than maxns N characters are discarded.
124 allowmergestagger : Bool, optional
125 Allow joining of staggered read pairs.
126 minovlen : Int % Range(0, None), optional
127 Minimum overlap length of forward and reverse reads for joining.
128 maxdiffs : Int % Range(0, None), optional
129 Maximum number of mismatches in the forward/reverse read overlap for
130 joining.
131 minmergelen : Int % Range(0, None), optional
132 Minimum length of the joined read to be retained.
133 maxmergelen : Int % Range(0, None), optional
134 Maximum length of the joined read to be retained.
135 maxee : Float % Range(0.0, None), optional
136 Maximum number of expected errors in the joined read to be retained.
137 qmin : Int % Range(-5, 2, inclusive_end=True), optional
138 The minimum allowed quality score in the input.
139 qminout : Int % Range(-5, 2, inclusive_end=True), optional
140 The minimum allowed quality score to use in output.
141 qmax : Int % Range(40, 41, inclusive_end=True), optional
142 The maximum allowed quality score in the input.
143 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
144 The maximum allowed quality score to use in output.
145
146 Returns
147 -------
148 joined_sequences : SampleData[JoinedSequencesWithQuality]
149 The joined sequences.
150 ]]>
151 </help>
152 </tool>