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comparison tools/fastq/fastq_paired_end_interlacer.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_interlacer" name="FASTQ interlacer" version="1.1">
2 <description>on paired end reads</description>
3 <command interpreter="python">fastq_paired_end_interlacer.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$outfile_pairs' '$outfile_singles'</command>
4 <inputs>
5 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />
6 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />
7 </inputs>
8 <outputs>
9 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->
10 <!-- $input1_file.id = ID , e.g. 10 -->
11 <!-- $input1_file.hid = history ID, e.g. 5 -->
12 <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from data ${input1_file.hid} and data ${input2_file.hid}"/>
13 <data name="outfile_singles" format="input" label="FASTQ interlacer singles from data ${input1_file.hid} and data ${input2_file.hid}"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
18 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
19 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" />
20 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" />
21 </test>
22 <test>
23 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
24 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
25 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" />
26 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" />
27 </test>
28 </tests>
29 <help>
30 **What it does**
31
32 This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file.
33
34 Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
35
36 -----
37
38 **Input**
39
40 Left-hand mates, for example::
41
42 @1539:931/1
43 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
44 +1539:931/1
45 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
46
47 Right-hand mates, for example::
48
49 @1539:931/2
50 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
51 +1539:931/2
52 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
53
54 -----
55
56 **Output**
57
58 A multiple-fastq file containing interlaced left and right paired reads::
59
60 @1539:931/1
61 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
62 +1539:931/1
63 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
64 @1539:931/2
65 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
66 +1539:931/2
67 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
68
69 A multiple-fastq file containing reads that have no mate is also produced.
70
71 </help>
72 </tool>