|
5
|
1 <tool id="extract_bcs.py" name="extract_bcs.py" version="1.0.0">
|
|
0
|
2 <description>Extract barcodes using pattern.</description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
|
7 <expand macro="stdio" />
|
|
|
8 <version_command>python extract_bcs.py --version</version_command>
|
|
|
9 <command interpreter="python"><![CDATA[
|
|
|
10 extract_bcs.py
|
|
|
11 #if $positional_1 and $positional_1 is not None:
|
|
|
12 $positional_1
|
|
|
13 #end if
|
|
|
14
|
|
|
15 #if $positional_2 and $positional_2 is not None:
|
|
|
16 $positional_2
|
|
|
17 #end if
|
|
|
18
|
|
5
|
19 --bcs $extractedbcs
|
|
|
20
|
|
0
|
21 > $default]]></command>
|
|
|
22 <inputs>
|
|
|
23 <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/>
|
|
|
24 <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/>
|
|
|
25 </inputs>
|
|
|
26 <outputs>
|
|
5
|
27 <data hidden="false" name="default" format="fastq"/>
|
|
|
28 <data name="extractedbcs" format="fasta"/>
|
|
0
|
29 </outputs>
|
|
|
30 <tests>
|
|
|
31 <test>
|
|
|
32 <param name="positional_1" value="reads.fastq"/>
|
|
|
33 <param name="positional_2" value="XXXNNXXX"/>
|
|
5
|
34 <output name="default" file="result_original_head.fastq"/>
|
|
|
35 <output name="extractedbcs" file="result.fa"/>
|
|
0
|
36 </test>
|
|
|
37 </tests>
|
|
|
38 <help><![CDATA[
|
|
|
39 Exract barcodes from a FASTQ file according to a user-specified pattern.
|
|
|
40
|
|
|
41 Author: Daniel Maticzka
|
|
|
42 Copyright: 2015
|
|
|
43 License: Apache
|
|
|
44 Email: maticzkd@informatik.uni-freiburg.de
|
|
|
45 Status: Testing
|
|
|
46 ]]></help>
|
|
|
47 <expand macro="citations" />
|
|
|
48 </tool>
|
