annotate qiime2/qiime_feature-classifier_extract-reads.xml @ 4:914fa4daf16a draft

Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 370e0b6e9826
children de4c22a52df4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Extract reads from reference</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime feature-classifier extract-reads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-sequences=$isequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --p-f-primer="$pfprimer"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12 --p-r-primer="$prprimer"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
4
florianbegusch
parents: 0
diff changeset
14 #if str($ptrunclen):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 --p-trunc-len=$ptrunclen
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17
4
florianbegusch
parents: 0
diff changeset
18 #if str($ptrimleft):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 --p-trim-left=$ptrimleft
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21
4
florianbegusch
parents: 0
diff changeset
22 #if str($pidentity):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 --p-identity=$pidentity
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25
4
florianbegusch
parents: 0
diff changeset
26 #if str($pminlength):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 --p-min-length=$pminlength
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29
4
florianbegusch
parents: 0
diff changeset
30 #if str($pmaxlength):
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 --p-max-length=$pmaxlength
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 --o-reads=oreads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 cp oreads.qza $oreads
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <param label="--p-f-primer: TEXT forward primer sequence [required]" name="pfprimer" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <param label="--p-r-primer: TEXT reverse primer sequence [required]" name="prprimer" optional="False" type="text"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 Extract reads from reference
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 ############################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 Extract sequencing-like reads from a reference database.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 \
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 f_primer : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 forward primer sequence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 r_primer : Str
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 reverse primer sequence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 trunc_len : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 read is cut to trunc_len if trunc_len is positive. Applied before
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 trim_left.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 trim_left : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 trim_left nucleotides are removed from the 5' end if trim_left is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 positive. Applied after trunc_len.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 identity : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 minimum combined primer match identity threshold.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 min_length : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 Minimum amplicon length. Shorter amplicons are discarded. Applied after
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 trimming and truncation, so be aware that trimming may impact sequence
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 retention. Set to zero to disable min length filtering.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 max_length : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 Maximum amplicon length. Longer amplicons are discarded. Applied before
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 trimming and truncation, so plan accordingly. Set to zero (default) to
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 disable max length filtering.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 reads : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 </tool>