Mercurial > repos > xuebing > sharplabtool
comparison tools/fastq/fastq_masker_by_quality.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9071e359b9a3 |
---|---|
1 <tool id="fastq_masker_by_quality" name="FASTQ Masker" version="1.0.0"> | |
2 <description>by quality score</description> | |
3 <command interpreter="python">fastq_masker_by_quality.py '$input_file' '$output_file' -f '${input_file.extension[len( 'fastq' ):]}' -s '${quality_score}' -c '${score_comparison}' | |
4 #if $mask_type.value == 'lowercase' | |
5 --lowercase | |
6 #else | |
7 -m '${mask_type}' | |
8 #end if | |
9 </command> | |
10 <inputs> | |
11 <param name="input_file" type="data" format="fastqsanger" label="File to mask" /> | |
12 <param name="mask_type" type="select" label="Mask input with"> | |
13 <option value="N">N's</option> | |
14 <option value="lowercase">Lowercase</option> | |
15 </param> | |
16 <param name="score_comparison" type="select" label="When score is"> | |
17 <option value="le" selected="True">Less than or equal</option> | |
18 <option value="lt">Less than</option> | |
19 <option value="eq">Equal to</option> | |
20 <option value="ne">Not Equal to</option> | |
21 <option value="ge">Greater than</option> | |
22 <option value="gt">Greater than or equal</option> | |
23 </param> | |
24 <param name="quality_score" type="integer" value="0" label="Quality score"/> | |
25 </inputs> | |
26 <outputs> | |
27 <data name="output_file" format="fastqsanger" /> | |
28 </outputs> | |
29 <tests> | |
30 <test> | |
31 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
32 <param name="mask_type" value="N" /> | |
33 <param name="score_comparison" value="le" /> | |
34 <param name="quality_score" value="20" /> | |
35 <output name="output_file" file="sanger_full_range_masked_N.fastqsanger" /> | |
36 </test> | |
37 <test> | |
38 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> | |
39 <param name="mask_type" value="lowercase" /> | |
40 <param name="score_comparison" value="le" /> | |
41 <param name="quality_score" value="20" /> | |
42 <output name="output_file" file="sanger_full_range_masked_lowercase.fastqsanger" /> | |
43 </test> | |
44 </tests> | |
45 <help> | |
46 **What it does** | |
47 | |
48 This tool allows masking base characters in FASTQ format files dependent upon user specified quality score value and comparison method. | |
49 | |
50 This tool is not available for use on color space (csSanger) formats. | |
51 | |
52 ------ | |
53 | |
54 **Citation** | |
55 | |
56 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ | |
57 | |
58 | |
59 </help> | |
60 </tool> |