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comparison fastq_paired_end_joiner.xml @ 1:ce853b881881 draft

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Uploaded version 2.0.0 of tool.
author devteam
date Mon, 07 Jul 2014 15:17:40 -0400
parents d86b8db06e05
children ab37758348d0
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0:d86b8db06e05 1:ce853b881881
1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0"> 1 <tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0">
2 <description>on paired end reads</description> 2 <description>on paired end reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements> 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' ):]}' '$output_file'</command> 6 <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command>
7 <inputs> 7 <inputs>
8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" /> 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" /> 9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
10 <param name="style" type="select" label="FASTQ Header Style">
11 <option value="old" selected="true">old</option>
12 <option value="new">new</option>
13 </param>
10 </inputs> 14 </inputs>
11 <outputs> 15 <outputs>
12 <data name="output_file" format="input" /> 16 <data name="output_file" format="input" />
13 </outputs> 17 </outputs>
14 <tests> 18 <tests>
19 </test> 23 </test>
20 </tests> 24 </tests>
21 <help> 25 <help>
22 **What it does** 26 **What it does**
23 27
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. 28 This tool joins paired end FASTQ reads from two separate files into a
25 29 single read in one file. The join is performed using sequence
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. 30 identifiers, allowing the two files to contain differing ordering. If
31 a sequence identifier does not appear in both files, it is excluded
32 from the output.
27 33
28 ----- 34 -----
29 35
30 **Input formats** 36 **Input formats**
37
38 Both old and new (from recent Illumina software) style FASTQ headers
39 are supported. The following example uses the "old" style.
31 40
32 Left-hand Read:: 41 Left-hand Read::
33 42
34 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 43 @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
35 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC 44 GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC
54 +HWI-EAS91_1_30788AAXX:7:21:1542:1758 63 +HWI-EAS91_1_30788AAXX:7:21:1542:1758
55 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR 64 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR
56 65
57 ------ 66 ------
58 67
59 **Citation** 68 **The "new" style**
60 69
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;`_ 70 Recent Illumina FASTQ headers are structured as follows::
62 71
72 @COORDS FLAGS
73 COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
74 FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
63 75
76 where the whitespace character between COORDS and FLAGS can be either
77 a space or a tab.
78
79 ------
80
81 **Credits**
82
83 This is an extended version (adds support for "new" style FASTQ headers)
84 of D. Blankenberg's fastq joiner:
85
86 `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;`_
87
88 New style header support added by Simone Leo &lt;simone.leo@crs4.it&gt;
64 </help> 89 </help>
65 </tool> 90 </tool>