Mercurial > repos > iuc > bctools_extract_barcodes
comparison extract_bcs.xml @ 0:ce2477cd3d95 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48
author | iuc |
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date | Tue, 14 Nov 2017 05:53:20 -0500 |
parents | |
children | ceb779d5be5b |
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-1:000000000000 | 0:ce2477cd3d95 |
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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> |