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comparison qiime2/qiime_vsearch_join-pairs.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_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.7"> 2 <tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs"
3 <description> - Join paired-end reads.</description> 3 version="2020.8">
4 <requirements> 4 <description>Join paired-end reads.</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 vsearch join-pairs 9 qiime vsearch join-pairs
9 10
10 --i-demultiplexed-seqs=$idemultiplexedseqs 11 --i-demultiplexed-seqs=$idemultiplexedseqs
11 12
12 #if str($ptruncqual): 13 #if str($ptruncqual):
13 --p-truncqual="$ptruncqual" 14 --p-truncqual=$ptruncqual
14 #end if 15 #end if
15 16 --p-minlen=$pminlen
16 #if str($pminlen):
17 --p-minlen=$pminlen
18 #end if
19 17
20 #if str($pmaxns): 18 #if str($pmaxns):
21 --p-maxns="$pmaxns" 19 --p-maxns=$pmaxns
22 #end if 20 #end if
23
24 #if $pallowmergestagger: 21 #if $pallowmergestagger:
25 --p-allowmergestagger 22 --p-allowmergestagger
26 #end if 23 #end if
27 24
28 #if str($pminovlen): 25 --p-minovlen=$pminovlen
29 --p-minovlen=$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
30 #end if 52 #end if
31 53
32 #if str($pmaxdiffs):
33 --p-maxdiffs=$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 str($pqmin):
49 --p-qmin=$pqmin
50 #end if
51
52 #if str($pqminout):
53 --p-qminout=$pqminout
54 #end if
55
56 #if str($pqmax):
57 --p-qmax=$pqmax
58 #end if
59
60 #if str($pqmaxout):
61 --p-qmaxout=$pqmaxout
62 #end if
63
64 --o-joined-sequences=ojoinedsequences
65 ; 54 ;
66 cp ojoinedsequences.qza $ojoinedsequences 55 cp ojoinedsequences.qza $ojoinedsequences
67 ]]></command> 56
68 <inputs> 57 ]]></command>
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"/> 58 <inputs>
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"/> 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" />
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"/> 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" />
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"/> 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" />
73 <param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean"/> 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" />
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"/> 63 <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
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"/> 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" />
83 </inputs> 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" />
84 <outputs> 73 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
85 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences"/> 74
86 </outputs> 75 </inputs>
87 <help><![CDATA[ 76
77 <outputs>
78 <data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences" />
79
80 </outputs>
81
82 <help><![CDATA[
88 Join paired-end reads. 83 Join paired-end reads.
89 ###################### 84 ###############################################################
90 85
91 Join paired-end sequence reads using vsearch's merge_pairs function. The 86 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 87 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
93 when working with older fastq sequence data. See the vsearch documentation 88 when working with older fastq sequence data. See the vsearch documentation
94 for details on how paired-end joining is performed, and for more 89 for details on how paired-end joining is performed, and for more
124 The minimum allowed quality score to use in output. 119 The minimum allowed quality score to use in output.
125 qmax : Int % Range(40, 41, inclusive_end=True), optional 120 qmax : Int % Range(40, 41, inclusive_end=True), optional
126 The maximum allowed quality score in the input. 121 The maximum allowed quality score in the input.
127 qmaxout : Int % Range(40, 41, inclusive_end=True), optional 122 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
128 The maximum allowed quality score to use in output. 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.
129 127
130 Returns 128 Returns
131 ------- 129 -------
132 joined_sequences : SampleData[JoinedSequencesWithQuality] 130 joined_sequences : SampleData[JoinedSequencesWithQuality]
133 The joined sequences. 131 The joined sequences.
134 ]]></help> 132 ]]></help>
135 <macros> 133 <macros>
136 <import>qiime_citation.xml</import> 134 <import>qiime_citation.xml</import>
137 </macros> 135 </macros>
138 <expand macro="qiime_citation"/> 136 <expand macro="qiime_citation"/>
139 </tool> 137 </tool>