root/galaxy-central/tools/fastq/fastq_paired_end_joiner.xml

リビジョン 2, 2.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0">
2  <description>on paired end reads</description>
3  <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file'</command>
4  <inputs>
5    <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" />
6    <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
7  </inputs>
8  <outputs>
9    <data name="output_file" format="input" />
10  </outputs>
11  <tests>
12    <test>
13      <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
14      <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
15      <output name="output_file" file="3.fastqsanger" />
16    </test>
17  </tests>
18  <help>
19**What it does**
20
21This tool joins paired end FASTQ reads from two separate files into a single read in one file. 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 excluded from the output.
22
23Sequence 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.
24
25-----
26
27**Input formats**
28
29Left-hand Read::
30
31    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
32    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
33    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
34    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
35
36Right-hand Read::
37
38    @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
39    GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
40    +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
41    hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
42
43-----
44
45**Output**
46
47A multiple-fastq file, for example::
48
49    @HWI-EAS91_1_30788AAXX:7:21:1542:1758
50    GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
51    +HWI-EAS91_1_30788AAXX:7:21:1542:1758
52    hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
53
54  </help>
55</tool>
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