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comparison qiime2/qiime_feature-classifier_extract-reads.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
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3:eda5df31da55 4:71f124e02000
3 <description> - Extract reads from reference</description> 3 <description> - Extract reads from reference</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8
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 $seq = 'database.qza'
16 #end if
17
18
8 qiime feature-classifier extract-reads 19 qiime feature-classifier extract-reads
9 20
10 --i-sequences=$isequences 21 --i-sequences=$seq
22
11 --p-f-primer="$pfprimer" 23 --p-f-primer="$pfprimer"
12 --p-r-primer="$prprimer" 24 --p-r-primer="$prprimer"
13 25
14 #if $ptrunclen: 26 #if str($ptrunclen):
15 --p-trunc-len=$ptrunclen 27 --p-trunc-len=$ptrunclen
16 #end if 28 #end if
17 29
18 #if $ptrimleft: 30 #if str($ptrimleft):
19 --p-trim-left=$ptrimleft 31 --p-trim-left=$ptrimleft
20 #end if 32 #end if
21 33
22 #if $pidentity: 34 #if str($pidentity):
23 --p-identity=$pidentity 35 --p-identity=$pidentity
24 #end if 36 #end if
25 37
26 #if $pminlength: 38 #if str($pminlength):
27 --p-min-length=$pminlength 39 --p-min-length=$pminlength
28 #end if 40 #end if
29 41
30 #if $pmaxlength: 42 #if str($pmaxlength):
31 --p-max-length=$pmaxlength 43 --p-max-length=$pmaxlength
32 #end if 44 #end if
33 45
34 --o-reads=oreads 46 --o-reads=oreads
35 ; 47 ;
36 cp oreads.qza $oreads 48 cp oreads.qza $oreads
37 ]]></command> 49 ]]></command>
38 <inputs> 50 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/> 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
40 <param label="--p-f-primer: TEXT forward primer sequence [required]" name="pfprimer" optional="False" type="text"/> 66 <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"/> 67 <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"/> 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"/>
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"/> 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"/>
44 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/> 70 <param label="--p-identity: NUMBER minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>