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annotate tools/fastq/fastq_paired_unpaired.txt @ 0:72e9fcaec61f

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Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:21:17 -0400
parents
children 7ed81e36fc1c
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72e9fcaec61f Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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1 Galaxy tool to divide FASTQ files into paired and unpaired reads
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2 ================================================================
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3
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4 This tool is copyright 2010 by Peter Cock, SCRI, UK. All rights reserved.
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5 See the licence text below.
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6
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7 This tool is a short Python script (using the Biopython library functions) which
72e9fcaec61f Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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8 divides a FASTQ file into paired reads, and single or orphan reads. You can have
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9 separate files for the forward/reverse reads, or have them interleaved in a
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10 single file.
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11
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12 Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
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13 Color Space should all work equally well).
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14
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15 There are just two files to install:
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16
72e9fcaec61f Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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17 * fastq_paired_unpaired.py (the Python script)
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18 * fastq_paired_unpaired.xml (the Galaxy tool definition)
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19
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20 The suggested location is in the Galaxy folder tools/fastq next to other FASTQ
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21 tools provided with Galaxy.
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22
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23 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
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24 the tool. One suggested location is next to the fastq_filter.xml entry. Simply
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25 add the line:
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26
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27 <tool file="fastq/fastq_paired_unpaired.xml" />
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28
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29 That's it.
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30
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31
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32 History
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33 =======
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34
72e9fcaec61f Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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35 v0.0.1 - Initial version, using Biopython
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36 v0.0.2 - Help text; cope with multiple pairs per template
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37 v0.0.3 - Galaxy XML wrappers added
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38 v0.0.4 - Use Galaxy library to handle FASTQ files (avoid Biopython dependency)
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39
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40
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41 Developers
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42 ==========
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43
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44 This script and other tools for filtering FASTA, FASTQ and SFF files are
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45 currently being developed on the following hg branch:
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46 http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
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47
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48 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
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49 the following command from the Galaxy root folder:
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50
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51 tar -czf fastq_paired_unpaired.tar.gz tools/fastq/fastq_paired_unpaired.*
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52
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53 Check this worked:
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54
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55 $ tar -tzf fastq_paired_unpaired.tar.gz
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56 fastq/fastq_paired_unpaired.py
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57 fastq/fastq_paired_unpaired.txt
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58 fastq/fastq_paired_unpaired.xml
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59
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60
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61 Licence (MIT/BSD style)
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62 =======================
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63
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64 Permission to use, copy, modify, and distribute this software and its
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65 documentation with or without modifications and for any purpose and
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66 without fee is hereby granted, provided that any copyright notices
72e9fcaec61f Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
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67 appear in all copies and that both those copyright notices and this
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68 permission notice appear in supporting documentation, and that the
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69 names of the contributors or copyright holders not be used in
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70 advertising or publicity pertaining to distribution of the software
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71 without specific prior permission.
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72
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73 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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74 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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75 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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76 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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77 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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78 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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79 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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80 OR PERFORMANCE OF THIS SOFTWARE.