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comparison qiime2/qiime_feature-classifier_extract-reads.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2018.4">
3 <description> - Extract reads from reference</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier extract-reads --i-sequences=$isequences --p-r-primer="$prprimer" --p-f-primer="$pfprimer"
9
10 #if $ptrunclen:
11 --p-trunc-len=$ptrunclen
12 #end if
13
14 #if str($cmdconfig) != 'None':
15 --cmd-config=$cmdconfig
16 #end if
17
18 #if $ptrimleft:
19 --p-trim-left=$ptrimleft
20 #end if
21 --o-reads=oreads
22 #if $pidentity:
23 --p-identity=$pidentity
24 #end if
25 ;
26 cp oreads.qza $oreads;
27 ]]></command>
28 <inputs>
29 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
30 <param label="--p-f-primer: forward primer sequence [required]" name="pfprimer" optional="False" type="text"/>
31 <param label="--p-r-primer: reverse primer sequence [required]" name="prprimer" optional="False" type="text"/>
32 <param label="--p-trunc-len: read is cut to trunc_len if trunc_len is positive. Applied before trim_left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
33 <param label="--p-trim-left: trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trunc_len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
34 <param label="--p-identity: minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
35 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
36 </inputs>
37 <outputs>
38 <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
39 </outputs>
40 <help><![CDATA[
41 Extract reads from reference
42 -----------------------------
43
44 Extract sequencing-like reads from a reference database.
45
46 Parameters
47 ----------
48 sequences : FeatureData[Sequence]
49
50 f_primer : Str
51 forward primer sequence
52 r_primer : Str
53 reverse primer sequence
54 trunc_len : Int, optional
55 read is cut to trunc_len if trunc_len is positive. Applied before
56 trim_left.
57 trim_left : Int, optional
58 trim_left nucleotides are removed from the 5' end if trim_left is
59 positive. Applied after trunc_len.
60 identity : Float, optional
61 minimum combined primer match identity threshold.
62
63 Returns
64 -------
65 reads : FeatureData[Sequence]
66 ]]>
67 </help>
68 <macros>
69 <import>qiime_citation.xml</import>
70 </macros>
71 <expand macro="qiime_citation" />
72 </tool>