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comparison qiime2/qiime_feature-classifier_extract-reads.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 914fa4daf16a
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.4">
3 <description> - Extract reads from reference</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier extract-reads
9
10 --i-sequences=$isequences
11 --p-f-primer="$pfprimer"
12 --p-r-primer="$prprimer"
13
14 #if $ptrunclen:
15 --p-trunc-len=$ptrunclen
16 #end if
17
18 #if $ptrimleft:
19 --p-trim-left=$ptrimleft
20 #end if
21
22 #if $pidentity:
23 --p-identity=$pidentity
24 #end if
25
26 #if $pminlength:
27 --p-min-length=$pminlength
28 #end if
29
30 #if $pmaxlength:
31 --p-max-length=$pmaxlength
32 #end if
33
34 --o-reads=oreads
35 ;
36 cp oreads.qza $oreads
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
40 <param label="--p-f-primer: TEXT forward primer sequence [required]" name="pfprimer" optional="False" type="text"/>
41 <param label="--p-r-primer: TEXT reverse primer sequence [required]" name="prprimer" optional="False" type="text"/>
42 <param label="--p-trunc-len: INTEGER read is cut to trunc-len if trunc-len is positive. Applied before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
43 <param label="--p-trim-left: INTEGER trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
44 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
45 <param label="--p-min-length: INTEGER Minimum amplicon length. Shorter amplicons are Range(0, None) discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering. [default: 50]" name="pminlength" optional="True" type="integer" min="0" value="50"/>
46 <param label="--p-max-length: INTEGER Maximum amplicon length. Longer amplicons are Range(0, None) discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering. [default: 0]" name="pmaxlength" optional="True" type="integer" min="0" value="0"/>
47 </inputs>
48 <outputs>
49 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
50 </outputs>
51 <help><![CDATA[
52 Extract reads from reference
53 ############################
54
55 Extract sequencing-like reads from a reference database.
56
57 Parameters
58 ----------
59 sequences : FeatureData[Sequence]
60 \
61
62 f_primer : Str
63 forward primer sequence
64 r_primer : Str
65 reverse primer sequence
66 trunc_len : Int, optional
67 read is cut to trunc_len if trunc_len is positive. Applied before
68 trim_left.
69 trim_left : Int, optional
70 trim_left nucleotides are removed from the 5' end if trim_left is
71 positive. Applied after trunc_len.
72 identity : Float, optional
73 minimum combined primer match identity threshold.
74 min_length : Int % Range(0, None), optional
75 Minimum amplicon length. Shorter amplicons are discarded. Applied after
76 trimming and truncation, so be aware that trimming may impact sequence
77 retention. Set to zero to disable min length filtering.
78 max_length : Int % Range(0, None), optional
79 Maximum amplicon length. Longer amplicons are discarded. Applied before
80 trimming and truncation, so plan accordingly. Set to zero (default) to
81 disable max length filtering.
82
83 Returns
84 -------
85 reads : FeatureData[Sequence]
86 ]]></help>
87 <macros>
88 <import>qiime_citation.xml</import>
89 </macros>
90 <expand macro="qiime_citation"/>
91 </tool>