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comparison tools/fastq/fastq_paired_end_deinterlacer.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1">
2 <description>on paired end reads</description>
3 <command interpreter="python">fastq_paired_end_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command>
4 <inputs>
5 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
6 </inputs>
7 <outputs>
8 <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
9 <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
10 <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
11 <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
12 </outputs>
13 <tests>
14 <test>
15 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
16 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" />
17 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" />
18 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" />
19 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" />
20 </test>
21 <test>
22 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
23 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" />
24 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" />
25 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" />
26 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" />
27 </test>
28 </tests>
29 <help>
30 **What it does**
31
32 De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.
33
34 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
35
36 -----
37
38 **Input**
39
40 A multiple-fastq file containing paired-end reads, for example::
41
42 @1539:931/1
43 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
44 +1539:931/1
45 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
46 @1539:931/2
47 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
48 +1539:931/2
49 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
50
51 -----
52
53 **Output**
54
55 Multi-fastq file with left-hand mate only::
56
57 @1539:931/1
58 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
59 +1539:931/1
60 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
61
62 Multi-fastq file with right-hand mate only::
63
64 @1539:931/2
65 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
66 +1539:931/2
67 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
68
69 </help>
70 </tool>