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comparison qiime2/qiime_feature-classifier_extract-reads.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_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.7"> 2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads"
3 <description> - Extract reads from reference</description> 3 version="2020.8">
4 <requirements> 4 <description>Extract reads from reference sequences.</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 8 <command><![CDATA[
9
10 #if str( $input_sequences.selector ) == 'history'
11 #set $seq = $input_sequences.i_sequences
12
13 #else:
14 qiime tools import --type 'FeatureData[Sequence]' --input-path '$input_sequences.i_sequences.fields.path' --output-path database.qza;
15 #set $seq = 'database.qza'
16 #end if
17
18
19 qiime feature-classifier extract-reads 9 qiime feature-classifier extract-reads
20 10
21 --i-sequences=$seq 11 --i-sequences=$isequences
22 12
23 --p-f-primer="$pfprimer" 13 --p-f-primer=$pfprimer
24 --p-r-primer="$prprimer"
25 14
26 #if str($ptrunclen): 15 --p-r-primer=$prprimer
27 --p-trunc-len=$ptrunclen
28 #end if
29 16
30 #if str($ptrimleft): 17 --p-trim-right=$ptrimright
31 --p-trim-left=$ptrimleft
32 #end if
33 18
34 #if str($pidentity): 19 --p-trunc-len=$ptrunclen
35 --p-identity=$pidentity
36 #end if
37 20
38 #if str($pminlength): 21 --p-trim-left=$ptrimleft
39 --p-min-length=$pminlength
40 #end if
41 22
42 #if str($pmaxlength): 23 --p-identity=$pidentity
43 --p-max-length=$pmaxlength 24
25 --p-min-length=$pminlength
26
27 --p-max-length=$pmaxlength
28
29 --p-n-jobs=$pnjobs
30
31 #if str($preadorientation) != 'None':
32 --p-read-orientation=$preadorientation
44 #end if 33 #end if
45 34
46 --o-reads=oreads 35 --o-reads=oreads
36
37 #if str($examples) != 'None':
38 --examples=$examples
39 #end if
40
47 ; 41 ;
48 cp oreads.qza $oreads 42 cp oreads.qza $oreads
49 ]]></command>
50 <inputs>
51 <conditional name="input_sequences" optional="False">
52 <param name="selector" type="select" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences to query">
53 <option value="cached">Public databases</option>
54 <option value="history">Databases from your history</option>
55 </param>
56 <when value="cached">
57 <param name="i_sequences" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences" type="select" optional="True">
58 <options from_data_table="qiime_rep_set" />
59 </param>
60 </when>
61 <when value="history">
62 <param name="i_sequences" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
63 </when>
64 </conditional>
65 43
66 <param label="--p-f-primer: TEXT forward primer sequence [required]" name="pfprimer" optional="False" type="text"/> 44 ]]></command>
67 <param label="--p-r-primer: TEXT reverse primer sequence [required]" name="prprimer" optional="False" type="text"/> 45 <inputs>
68 <param label="--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/> 46 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data" />
69 <param label="--p-trim-left: INTEGER trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/> 47 <param label="--p-f-primer: TEXT forward primer sequence (5\' -&gt; 3\'). [required]" name="pfprimer" optional="False" type="text" />
70 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/> 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" />
71 <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]" name="pminlength" optional="True" type="integer" min="0" value="50"/> 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" />
72 <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]" name="pmaxlength" optional="True" type="integer" min="0" 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" />
73 </inputs> 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" />
74 <outputs> 52 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8" />
75 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/> 53 <param label="--p-min-length: INTEGER Minimum amplicon length. Shorter amplicons are Range(0, None) discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering. [default: 50]" min="0" name="pminlength" optional="True" type="integer" value="50" />
76 </outputs> 54 <param label="--p-max-length: INTEGER Maximum amplicon length. Longer amplicons are Range(0, None) discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering. [default: 0]" min="0" name="pmaxlength" optional="True" type="integer" value="0" />
77 <help><![CDATA[ 55 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
78 Extract reads from reference 56 <option selected="True" value="None">Selection is Optional</option>
79 ############################ 57 <option value="both">both</option>
58 <option value="forward">forward</option>
59 <option value="reverse">reverse</option>
60 </param>
61 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
62
63 </inputs>
80 64
81 Extract sequencing-like reads from a reference database. 65 <outputs>
66 <data format="qza" label="${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.
82 84
83 Parameters 85 Parameters
84 ---------- 86 ----------
85 sequences : FeatureData[Sequence] 87 sequences : FeatureData[Sequence]
86 \
87
88 f_primer : Str 88 f_primer : Str
89 forward primer sequence 89 forward primer sequence (5' -> 3').
90 r_primer : Str 90 r_primer : Str
91 reverse primer sequence 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.
92 trunc_len : Int, optional 96 trunc_len : Int, optional
93 read is cut to trunc_len if trunc_len is positive. Applied before 97 read is cut to trunc_len if trunc_len is positive. Applied after
94 trim_left. 98 trim_right but before trim_left.
95 trim_left : Int, optional 99 trim_left : Int, optional
96 trim_left nucleotides are removed from the 5' end if trim_left is 100 trim_left nucleotides are removed from the 5' end if trim_left is
97 positive. Applied after trunc_len. 101 positive. Applied after trim_right and trunc_len.
98 identity : Float, optional 102 identity : Float, optional
99 minimum combined primer match identity threshold. 103 minimum combined primer match identity threshold.
100 min_length : Int % Range(0, None), optional 104 min_length : Int % Range(0, None), optional
101 Minimum amplicon length. Shorter amplicons are discarded. Applied after 105 Minimum amplicon length. Shorter amplicons are discarded. Applied after
102 trimming and truncation, so be aware that trimming may impact sequence 106 trimming and truncation, so be aware that trimming may impact sequence
103 retention. Set to zero to disable min length filtering. 107 retention. Set to zero to disable min length filtering.
104 max_length : Int % Range(0, None), optional 108 max_length : Int % Range(0, None), optional
105 Maximum amplicon length. Longer amplicons are discarded. Applied before 109 Maximum amplicon length. Longer amplicons are discarded. Applied before
106 trimming and truncation, so plan accordingly. Set to zero (default) to 110 trimming and truncation, so plan accordingly. Set to zero (default) to
107 disable max length filtering. 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.
108 121
109 Returns 122 Returns
110 ------- 123 -------
111 reads : FeatureData[Sequence] 124 reads : FeatureData[Sequence]
112 ]]></help> 125 ]]></help>
113 <macros> 126 <macros>
114 <import>qiime_citation.xml</import> 127 <import>qiime_citation.xml</import>
115 </macros> 128 </macros>
116 <expand macro="qiime_citation"/> 129 <expand macro="qiime_citation"/>
117 </tool> 130 </tool>