Mercurial > repos > peterjc > fastq_paired_unpaired

comparison tools/fastq/fastq_paired_unpaired.txt @ 2:95a632a71951 draft

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Uploaded v0.0.6, adds unit test
author peterjc
date Tue, 30 Apr 2013 14:08:37 -0400
parents 7ed81e36fc1c
children
comparison
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1:7ed81e36fc1c 2:95a632a71951
35 v0.0.1 - Initial version, using Biopython 35 v0.0.1 - Initial version, using Biopython
36 v0.0.2 - Help text; cope with multiple pairs per template 36 v0.0.2 - Help text; cope with multiple pairs per template
37 v0.0.3 - Galaxy XML wrappers added 37 v0.0.3 - Galaxy XML wrappers added
38 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency) 38 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
39 v0.0.5 - Handle Illumina 1.8 style pair names 39 v0.0.5 - Handle Illumina 1.8 style pair names
40 v0.0.6 - Record script version when run from Galaxy
41 - Added unit test (FASTQ file using Sanger naming)
40 42
41 43
42 Developers 44 Developers
43 ========== 45 ==========
44 46
45 This script and other tools for filtering FASTA, FASTQ and SFF files are 47 This script and other tools for filtering FASTA, FASTQ and SFF files are
46 currently being developed on the following hg branch: 48 currently being developed on the following hg branch:
47 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter 49 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
48 50
49 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 51 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
50 the following command from the Galaxy root folder: 52 the following command from the Galaxy root folder:
51 53
52 tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* 54 $ tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.* test-data/sanger-pairs-*.fastq
53 55
54 Check this worked: 56 Check this worked:
55 57
56 $ tar -tzf fastq_paired_unpaired.tar.gz 58 $ tar -tzf fastq_paired_unpaired.tar.gz
57 fastq/fastq_paired_unpaired.py 59 fastq/fastq_paired_unpaired.py
58 fastq/fastq_paired_unpaired.txt 60 fastq/fastq_paired_unpaired.txt
59 fastq/fastq_paired_unpaired.xml 61 fastq/fastq_paired_unpaired.xml
62 test-data/sanger-pairs-forward.fastq
63 test-data/sanger-pairs-interleaved.fastq
64 test-data/sanger-pairs-mixed.fastq
65 test-data/sanger-pairs-reverse.fastq
66 test-data/sanger-pairs-singles.fastq
60 67
61 68
62 Licence (MIT/BSD style) 69 Licence (MIT/BSD style)
63 ======================= 70 =======================
64 71