Mercurial > repos > peterjc > sff_filter_by_id
annotate tools/filters/sff_filter_by_id.xml @ 1:9cd3591f6afa default tip
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:25:08 -0400 |
parents | eb852527b26c |
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Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
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1 <tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.2" hidden="true"> |
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2 <description>from a tabular file</description> |
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3 <command interpreter="python"> |
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4 sff_filter_by_id.py $input_tabular $columns $input_sff |
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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_sff" type="data" format="sff" label="SFF file to filter on the identifiers"/> |
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15 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing SFF identifiers"/> |
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16 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing SFF 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 SFF files</option> |
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22 <option value="pos">Just positive matches (ID on list), as a single SFF file</option> |
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23 <option value="neg">Just negative matches (ID not on list), as a single SFF 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="sff" label="With matched ID"> |
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33 <filter>output_choice_cond["output_choice"] != "neg"</filter> |
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34 </data> |
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35 <data name="output_neg" format="sff" label="Without matched ID"> |
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36 <filter>output_choice_cond["output_choice"] != "pos"</filter> |
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37 </data> |
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38 </outputs> |
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39 <tests> |
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40 </tests> |
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41 <requirements> |
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42 <requirement type="python-module">Bio</requirement> |
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43 </requirements> |
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44 <help> |
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45 |
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46 **Deprecated** |
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47 |
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48 This tool is now obsolete, and should not be used in future. It has been |
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49 replaced by a more general version covering FASTA, FASTQ and SFF in one |
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50 single tool. |
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51 |
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52 **What it does** |
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53 |
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54 By default it divides a Standard Flowgram Format (SFF) file in two, those |
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55 sequences with or without an ID present in the tabular file column(s) specified. |
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56 You can opt to have a single output file of just the matching records, or just |
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57 the non-matching ones. |
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58 |
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59 Note that the order of sequences in the original SFF file is preserved, as is |
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60 any Roche XML Manifest. Also, if any sequences share an identifier (which would |
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61 be very unusual in SFF files, duplicates are not removed). |
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62 |
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63 **Example Usage** |
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64 |
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65 You may have performed some kind of contamination search, for example running |
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66 BLASTN against a database of cloning vectors or bacteria, giving you a tabular |
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67 file containing read identifiers. You could use this tool to extract only the |
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68 reads without BLAST matches (i.e. those which do not match your contaminant |
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69 database). |
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70 |
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71 **Citation** |
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72 |
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73 This tool uses Biopython to read and write SFF files. If you use this tool in |
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74 scientific work leading to a publication, please cite the Biopython application |
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75 note: |
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76 |
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77 Cock et al 2009. Biopython: freely available Python tools for computational |
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78 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
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79 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
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80 |
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81 </help> |
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82 </tool> |