Mercurial > repos > peterjc > seq_filter_by_id
annotate tools/filters/seq_filter_by_id.xml @ 0:5844f6a450ed
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 17:24:30 -0400 |
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children | 262f08104540 |
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1 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.0.1"> |
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2 <description>from a tabular file</description> |
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3 <command interpreter="python"> |
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4 seq_filter_by_id.py $input_tabular $columns $input_file $input_file.ext |
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5 #if $output_choice_cond.output_choice=="both" |
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6 $output_pos $output_neg |
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7 #elif $output_choice_cond.output_choice=="pos" |
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8 $output_pos - |
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9 #elif $output_choice_cond.output_choice=="neg" |
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10 - $output_neg |
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11 #end if |
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12 </command> |
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13 <inputs> |
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14 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to filter on the identifiers" description="FASTA, FASTQ, or SFF format." /> |
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15 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
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16 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing sequence identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> |
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17 <validator type="no_options" message="Pick at least one column"/> |
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18 </param> |
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19 <conditional name="output_choice_cond"> |
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20 <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> |
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21 <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two files</option> |
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22 <option value="pos">Just positive matches (ID on list), as a single file</option> |
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23 <option value="neg">Just negative matches (ID not on list), as a single file</option> |
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24 </param> |
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25 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> |
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26 <when value="both" /> |
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27 <when value="pos" /> |
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28 <when value="neg" /> |
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29 </conditional> |
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30 </inputs> |
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31 <outputs> |
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32 <data name="output_pos" format="fasta" label="With matched ID"> |
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33 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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34 <change_format> |
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35 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
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36 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
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37 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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38 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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39 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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40 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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41 </change_format> |
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42 <filter>output_choice_cond["output_choice"] != "neg"</filter> |
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43 </data> |
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44 <data name="output_neg" format="fasta" label="Without matched ID"> |
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45 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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46 <change_format> |
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47 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
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48 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
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49 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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50 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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51 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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52 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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53 </change_format> |
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54 <filter>output_choice_cond["output_choice"] != "pos"</filter> |
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55 </data> |
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56 </outputs> |
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57 <tests> |
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58 </tests> |
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59 <requirements> |
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60 <requirement type="python-module">Bio</requirement> |
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61 </requirements> |
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62 <help> |
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63 |
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64 **What it does** |
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65 |
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66 By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in |
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67 two, those sequences with or without an ID present in the tabular file column(s) |
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68 specified. You can opt to have a single output file of just the matching records, |
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69 or just the non-matching ones. |
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70 |
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71 Note that the order of sequences in the original sequence file is preserved, as |
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72 is any Roche XML Manifest in an SFF file. Also, if any sequences share an |
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73 identifier (which would be very unusual in SFF files), duplicates are not removed. |
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74 |
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75 **Example Usage** |
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76 |
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77 You may have performed some kind of contamination search, for example running |
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78 BLASTN against a database of cloning vectors or bacteria, giving you a tabular |
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79 file containing read identifiers. You could use this tool to extract only the |
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80 reads without BLAST matches (i.e. those which do not match your contaminant |
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81 database). |
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82 |
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83 You may have a file of FASTA sequences which has been run some some analysis |
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84 tool giving tabular output, which has then been filtered on some criteria. |
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85 You can then use this tool to divide the original FASTA file into those entries |
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86 matching or not matching your criteria (those with or without their identifier |
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87 in the filtered tabular file). |
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88 |
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89 **Citation** |
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90 |
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91 This tool uses Biopython to read and write SFF files. If you use this tool in |
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92 scientific work leading to a publication, please cite the Biopython application |
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93 note (and Galaxy too of course): |
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94 |
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95 Cock et al 2009. Biopython: freely available Python tools for computational |
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96 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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97 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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98 |
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99 </help> |
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100 </tool> |