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comparison extract_bcs.xml @ 2:de4ea3aa1090 draft

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author rnateam
date Thu, 22 Oct 2015 10:26:45 -0400
parents 119fccb59597
children bf5b606f1aa7
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1:ae0f58d3318f 2:de4ea3aa1090
1 <tool id="extract_bcs.py" name="extract_bcs.py" version="1.0">
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
19 > $default]]></command>
20 <inputs>
21 <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/>
22 <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"/>
23 </inputs>
24 <outputs>
25 <data hidden="false" name="default" format="fastq" />
26 </outputs>
27 <tests>
28 <test>
29 <param name="positional_1" value="reads.fastq"/>
30 <param name="positional_2" value="XXXNNXXX"/>
31 <output name="default" file="result.fastq"/>
32 </test>
33 </tests>
34 <help><![CDATA[
35 Exract barcodes from a FASTQ file according to a user-specified pattern.
36
37 Author: Daniel Maticzka
38 Copyright: 2015
39 License: Apache
40 Email: maticzkd@informatik.uni-freiburg.de
41 Status: Testing
42 ]]></help>
43 <expand macro="citations" />
44 </tool>