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comparison fastq_paired_end_joiner.xml @ 0:2793d1d765b9 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:25:44 -0500
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1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0">
2 <description>on paired end reads</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements>
6 <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>
7 <inputs>
8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" />
9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
10 </inputs>
11 <outputs>
12 <data name="output_file" format="input" />
13 </outputs>
14 <tests>
15 <test>
16 <param name="input1_file" value="split_pair_reads_1.fastqsanger" ftype="fastqsanger" />
17 <param name="input2_file" value="split_pair_reads_2.fastqsanger" ftype="fastqsanger" />
18 <output name="output_file" file="3.fastqsanger" />
19 </test>
20 </tests>
21 <help>
22 **What it does**
23
24 This 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.
25
26 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.
27
28 -----
29
30 **Input formats**
31
32 Left-hand Read::
33
34 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
35 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
36 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
37 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
38
39 Right-hand Read::
40
41 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
42 GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
43 +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2
44 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
45
46 -----
47
48 **Output**
49
50 A multiple-fastq file, for example::
51
52 @HWI-EAS91_1_30788AAXX:7:21:1542:1758
53 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA
54 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
55 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
56
57 ------
58
59 **Citation**
60
61 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
62
63
64 </help>
65 </tool>