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comparison qiime2/qiime_feature-classifier_extract-reads.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_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads"
3 version="2020.8">
4 <description>Extract reads from reference sequences.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-classifier extract-reads
10
11 --i-sequences=$isequences
12
13 --p-f-primer=$pfprimer
14
15 --p-r-primer=$prprimer
16
17 --p-trim-right=$ptrimright
18
19 --p-trunc-len=$ptrunclen
20
21 --p-trim-left=$ptrimleft
22
23 --p-identity=$pidentity
24
25 --p-min-length=$pminlength
26
27 --p-max-length=$pmaxlength
28
29 --p-n-jobs=$pnjobs
30
31 #if str($preadorientation) != 'None':
32 --p-read-orientation=$preadorientation
33 #end if
34
35 --o-reads=oreads
36
37 #if str($examples) != 'None':
38 --examples=$examples
39 #end if
40
41 ;
42 cp oreads.qza $oreads
43
44 ]]></command>
45 <inputs>
46 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data" />
47 <param label="--p-f-primer: TEXT forward primer sequence (5\' -&gt; 3\'). [required]" name="pfprimer" optional="False" type="text" />
48 <param label="--p-r-primer: TEXT reverse primer sequence (5\' -&gt; 3\'). Do not use reverse-complemented primer sequence. [required]" name="prprimer" optional="False" type="text" />
49 <param label="--p-trim-right: INTEGER trim-right nucleotides are removed from the 3\' end if trim-right is positive. Applied before trunc-len and trim-left. [default: 0]" name="ptrimright" optional="True" type="integer" value="0" />
50 <param label="--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0" />
51 <param label="--p-trim-left: INTEGER trim-left nucleotides are removed from the 5\' end if trim-left is positive. Applied after trim-right and trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0" />
52 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8" />
53 <param label="--p-min-length: INTEGER Minimum amplicon length. Shorter amplicons are Range(0, None) discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering. [default: 50]" min="0" name="pminlength" optional="True" type="integer" value="50" />
54 <param label="--p-max-length: INTEGER Maximum amplicon length. Longer amplicons are Range(0, None) discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering. [default: 0]" min="0" name="pmaxlength" optional="True" type="integer" value="0" />
55 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
56 <option selected="True" value="None">Selection is Optional</option>
57 <option value="both">both</option>
58 <option value="forward">forward</option>
59 <option value="reverse">reverse</option>
60 </param>
61 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
62
63 </inputs>
64
65 <outputs>
66 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads" />
67
68 </outputs>
69
70 <help><![CDATA[
71 Extract reads from reference sequences.
72 ###############################################################
73
74 Extract simulated amplicon reads from a reference database. Performs in-
75 silico PCR to extract simulated amplicons from reference sequences that
76 match the input primer sequences (within the mismatch threshold specified
77 by `identity`). Both primer sequences must be in the 5' -> 3' orientation.
78 Sequences that fail to match both primers will be excluded. Reads are
79 extracted, trimmed, and filtered in the following order: 1. reads are
80 extracted in specified orientation; 2. primers are removed; 3. reads longer
81 than `max_length` are removed; 4. reads are trimmed with `trim_right`; 5.
82 reads are truncated to `trunc_len`; 6. reads are trimmed with `trim_left`;
83 7. reads shorter than `min_length` are removed.
84
85 Parameters
86 ----------
87 sequences : FeatureData[Sequence]
88 f_primer : Str
89 forward primer sequence (5' -> 3').
90 r_primer : Str
91 reverse primer sequence (5' -> 3'). Do not use reverse-complemented
92 primer sequence.
93 trim_right : Int, optional
94 trim_right nucleotides are removed from the 3' end if trim_right is
95 positive. Applied before trunc_len and trim_left.
96 trunc_len : Int, optional
97 read is cut to trunc_len if trunc_len is positive. Applied after
98 trim_right but before trim_left.
99 trim_left : Int, optional
100 trim_left nucleotides are removed from the 5' end if trim_left is
101 positive. Applied after trim_right and trunc_len.
102 identity : Float, optional
103 minimum combined primer match identity threshold.
104 min_length : Int % Range(0, None), optional
105 Minimum amplicon length. Shorter amplicons are discarded. Applied after
106 trimming and truncation, so be aware that trimming may impact sequence
107 retention. Set to zero to disable min length filtering.
108 max_length : Int % Range(0, None), optional
109 Maximum amplicon length. Longer amplicons are discarded. Applied before
110 trimming and truncation, so plan accordingly. Set to zero (default) to
111 disable max length filtering.
112 n_jobs : Int % Range(1, None), optional
113 Number of seperate processes to run.
114 batch_size : Int % Range(1, None) | Str % Choices('auto'), optional
115 Number of sequences to process in a batch. The `auto` option is
116 calculated from the number of sequences and number of jobs specified.
117 read_orientation : Str % Choices('both', 'forward', 'reverse'), optional
118 Orientation of primers relative to the sequences: "forward" searches
119 for primer hits in the forward direction, "reverse" searches reverse-
120 complement, and "both" searches both directions.
121
122 Returns
123 -------
124 reads : FeatureData[Sequence]
125 ]]></help>
126 <macros>
127 <import>qiime_citation.xml</import>
128 </macros>
129 <expand macro="qiime_citation"/>
130 </tool>