Mercurial > repos > peterjc > seq_select_by_id
annotate tools/seq_select_by_id/seq_select_by_id.xml @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
author | peterjc |
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date | Wed, 13 May 2015 10:56:29 -0400 |
parents | 6842c0c7bc70 |
children | a5602454b0ad |
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6 | 1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11"> |
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2 <description>from a tabular file</description> |
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3 <requirements> |
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4 <requirement type="package" version="1.62">biopython</requirement> |
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5 <requirement type="python-module">Bio</requirement> |
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6 </requirements> |
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7 <stdio> |
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8 <!-- Anything other than zero is an error --> |
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9 <exit_code range="1:" /> |
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10 <exit_code range=":-1" /> |
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11 </stdio> |
6 | 12 <version_command interpreter="python">seq_select_by_id.py --version</version_command> |
13 <command interpreter="python"> | |
14 seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file" | |
15 </command> | |
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16 <inputs> |
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17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> |
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18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
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19 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |
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20 </inputs> |
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21 <outputs> |
6 | 22 <data name="output_file" format_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/> |
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23 </outputs> |
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24 <tests> |
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25 <test> |
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26 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> |
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27 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> |
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28 <param name="column" value="1" /> |
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29 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> |
6 | 30 <assert_stdout> |
31 <has_line line="Indexed 10 sequences" /> | |
32 <has_line line="Selected 1 sequences by ID" /> | |
33 </assert_stdout> | |
34 </test> | |
35 <!-- this version has white space in the identifier column (id and description) --> | |
36 <test> | |
37 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> | |
38 <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" /> | |
39 <param name="column" value="1" /> | |
40 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> | |
41 <assert_stdout> | |
42 <has_line line="Indexed 10 sequences" /> | |
43 <has_line line="Selected 1 sequences by ID" /> | |
44 </assert_stdout> | |
45 <assert_stderr> | |
46 <has_line line="WARNING: Some of your identifiers had white space in them, using first word only. e.g.:" /> | |
47 </assert_stderr> | |
48 </test> | |
49 <test expect_failure="true" expect_exit_code="1"> | |
50 <param name="input_file" value="empty.fasta" ftype="fasta" /> | |
51 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> | |
52 <param name="column" value="1" /> | |
53 <assert_stdout> | |
54 <has_line line="Indexed 0 sequences" /> | |
55 </assert_stdout> | |
56 <assert_stderr> | |
57 <has_line line="Identifier 'gi|16127999|ref|NP_414546.1|' not found in sequence file" /> | |
58 </assert_stderr> | |
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59 </test> |
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60 </tests> |
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61 <help> |
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62 **What it does** |
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63 |
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64 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a |
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65 new sequence file (of the same format) containing only the records with identifiers |
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66 in the tabular file (in the order from the tabular file). |
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67 |
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68 WARNING: If you have any duplicates in the tabular file identifiers, you will get |
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69 duplicate sequences in the output. |
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70 |
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71 **References** |
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72 |
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73 If you use this Galaxy tool in work leading to a scientific publication please |
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74 cite the following papers: |
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75 |
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76 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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77 Galaxy tools and workflows for sequence analysis with applications |
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78 in molecular plant pathology. PeerJ 1:e167 |
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79 http://dx.doi.org/10.7717/peerj.167 |
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80 |
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81 This tool uses Biopython to read, write and index sequence files, so you may |
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82 also wish to cite the Biopython application note (and Galaxy too of course): |
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83 |
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84 Cock et al (2009). Biopython: freely available Python tools for computational |
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85 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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86 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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87 |
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88 This tool is available to install into other Galaxy Instances via the Galaxy |
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89 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id |
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90 </help> |
6 | 91 <citations> |
92 <citation type="doi">10.7717/peerj.167</citation> | |
93 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
94 </citations> | |
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95 </tool> |