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annotate tools/fasta_tools/fasta_filter_by_id.xml @ 1:5cd569750e85

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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:22:48 -0400
parents 2e5f8ad1a096
children 5b552b3005f2
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5cd569750e85 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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1 <tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.3">
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2 <description>from a tabular file</description>
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3 <command interpreter="python">
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4 fasta_filter_by_id.py $input_tabular $columns $input_fasta
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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_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/>
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15 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA identifiers"/>
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16 <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA 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 FASTA files</option>
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22 <option value="pos">Just positive matches (ID on list), as a single FASTA file</option>
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23 <option value="neg">Just negative matches (ID not on list), as a single FASTA 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 <filter>output_choice_cond["output_choice"] != "neg"</filter>
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34 </data>
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35 <data name="output_neg" format="fasta" 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 <!-- Can't get these unit tests to run, may be a Galaxy problem
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41 <test>
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42 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
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43 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
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44 <param name="columns" value="1" />
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45 <param name="output_choice" value="both" />
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46 <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
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47 <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
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48 </test>
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49 <test>
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50 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
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51 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
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52 <param name="columns" value="1" />
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53 <param name="output_choice" value="pos" />
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54 <output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
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55 </test>
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56 <test>
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57 <param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
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58 <param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
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59 <param name="columns" value="1" />
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60 <param name="output_choice" value="neg" />
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61 <output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
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62 </test>
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63 -->
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64 </tests>
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65 <help>
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66
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67 **What it does**
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68
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69 By default it divides a FASTA file in two, those sequences with or without an
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70 ID present in the tabular file column(s) specified. You can opt to have a
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71 single output file of just the matching records, or just the non-matching ones.
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72
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73 Note that the order of sequences in the original FASTA file is preserved.
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74 Also, if any sequences share an identifier, duplicates are not removed.
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75
1
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76 **Example Usage**
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77
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78 Given a FASTA file of proteins you might run a signal peptide search (e.g.
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79 via the SignalP wrapper for Galaxy), then filtered these tabular results to
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80 select just those with a signal peptide. You could then use this tool to get
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81 a FASTA file of only the proteins with predicted signal peptides.
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82
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83 </help>
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84 </tool>