Mercurial > repos > iuc > bctools_extract_barcodes

comparison extract_bcs.xml @ 0:8fbf997d64c0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author iuc
date Tue, 14 Nov 2017 05:50:52 -0500
parents
children 47262bbf8904
comparison
equal deleted inserted replaced
-1:000000000000 0:8fbf997d64c0
1 <tool id="bctools_extract_barcodes" name="Extract barcodes" version="@VERSION@">
2 <description>according to pattern</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 extract_bcs.py
9 '$reads'
10 #if $barcode_pattern and $barcode_pattern is not None:
11 '$barcode_pattern'
12 #end if
13 --bcs '$extracted_barcodes'
14 > '$reads_cleaned'
15 ]]></command>
16 <inputs>
17 <param name="reads" type="data" format="fastq" label="Barcoded sequences" />
18 <param name="barcode_pattern" type="text" label="Pattern for extracting barcode nucleotides" help="Starting at 5'-end. X positions will be moved to a separate file, N positions will be kept.">
19 <sanitizer invalid_char="N">
20 <valid initial="none">
21 <add value="X"/>
22 <add value="N"/>
23 </valid>
24 </sanitizer>
25 </param>
26 </inputs>
27 <outputs>
28 <data name="reads_cleaned" format="fastq"/>
29 <data name="extracted_barcodes" format="fastq"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="reads" value="reads.fastq"/>
34 <param name="barcode_pattern" value="XXXNNXXX"/>
35 <output name="reads_cleaned" file="result_original_head.fastq"/>
36 <output name="extracted_barcodes" file="extracted_bcs.fastq"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40
41 bctools - Extract barcodes according to pattern
42 ===============================================
43
44 Exract barcodes from a FASTQ file according to a user-specified pattern and write them to a separate FASTQ file.
45
46 ]]></help>
47 <expand macro="citations"/>
48 </tool>