Mercurial > repos > peterjc > seq_select_by_id
annotate tools/filters/seq_select_by_id.txt @ 0:838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:38 -0400 |
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children | 50a8a6917a9c |
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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 Galaxy tool to select FASTA, FASTQ or SFF sequences by ID |
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2 ========================================================= |
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3 |
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4 This tool is copyright 2011 by Peter Cock, The James Hutton Institute |
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5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
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6 See the licence text below. |
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7 |
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8 This tool is a short Python script (using Biopython library functions) to extract |
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9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given |
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10 by a column of a tabular file. The output order follows that of the tabular file, |
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11 and if there are duplicates in the tabular file, there will be duplicates in the |
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12 output sequence file. |
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13 |
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14 See also the sister tool to filter sequence files according to IDs from column(s) |
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15 of a tabular file, where the output order follows the sequence file, and any |
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16 duplicate IDs are ignored. |
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17 |
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18 There are just two files to install: |
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19 |
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20 * seq_select_by_id.py (the Python script) |
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21 * seq_select_by_id.xml (the Galaxy tool definition) |
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22 |
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23 The suggested location is in the Galaxy folder tools/filters next to the tool |
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24 for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. |
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25 |
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26 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the |
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27 tool. One suggested location is in the filters section. Simply add the line: |
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28 |
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29 <tool file="filters/sff_select_by_id.xml" /> |
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30 |
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31 You will also need to install Biopython 1.54 or later. That's it. |
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32 |
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33 |
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34 History |
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35 ======= |
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36 |
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37 v0.0.1 - Initial version. |
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38 |
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39 |
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40 Developers |
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41 ========== |
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42 |
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43 This script and related tools are being developed on the following hg branch: |
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44 http://bitbucket.org/peterjc/galaxy-central/src/tools |
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45 |
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46 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use |
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47 the following command from the Galaxy root folder: |
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48 |
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49 tar -czf seq_select_by_id.tar.gz tools/filters/seq_select_by_id.* |
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50 |
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51 Check this worked: |
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52 |
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53 $ tar -tzf seq_select_by_id.tar.gz |
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54 filter/seq_select_by_id.py |
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55 filter/seq_select_by_id.txt |
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56 filter/seq_select_by_id.xml |
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57 |
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58 |
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59 Licence (MIT/BSD style) |
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60 ======================= |
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61 |
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62 Permission to use, copy, modify, and distribute this software and its |
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63 documentation with or without modifications and for any purpose and |
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64 without fee is hereby granted, provided that any copyright notices |
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65 appear in all copies and that both those copyright notices and this |
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66 permission notice appear in supporting documentation, and that the |
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67 names of the contributors or copyright holders not be used in |
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68 advertising or publicity pertaining to distribution of the software |
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69 without specific prior permission. |
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70 |
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71 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL |
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72 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED |
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73 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE |
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74 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT |
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75 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS |
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76 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE |
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77 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE |
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78 OR PERFORMANCE OF THIS SOFTWARE. |