Mercurial > repos > peterjc > fastq_filter_by_id
annotate tools/fastq/fastq_filter_by_id.xml @ 1:b79caa511ba2
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:23:49 -0400 |
parents | 10e963c79a45 |
children | d570cc324779 |
rev | line source |
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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
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1 <tool id="fastq_filter_by_id" name="Filter FASTQ 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 fastq_filter_by_id.py $input_tabular $columns $input_fastq |
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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_fastq" type="data" format="fastq" label="FASTQ file to filter on the identifiers"/> |
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15 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTQ 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="fastq" 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_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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36 <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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37 <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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38 <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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39 </change_format> |
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40 <filter>output_choice_cond["output_choice"] != "neg"</filter> |
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41 </data> |
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42 <data name="output_neg" format="fastq" label="Without matched ID"> |
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43 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
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44 <change_format> |
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45 <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
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46 <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
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47 <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
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48 <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
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49 </change_format> |
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50 <filter>output_choice_cond["output_choice"] != "pos"</filter> |
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51 </data> |
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52 </outputs> |
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53 <tests> |
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54 </tests> |
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55 <help> |
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56 |
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57 **What it does** |
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58 |
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59 By default it divides a FASTQ file in two, those sequences with or without an |
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60 ID present in the tabular file column(s) specified. You can opt to have a |
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61 single output file of just the matching records, or just the non-matching ones. |
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62 |
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63 Note that the order of sequences in the original FASTQ file is preserved. |
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64 Also, if any sequences share an identifier, duplicates are not removed. |
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65 |
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66 **Example Usage** |
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67 |
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68 You may have mapped your reads against a reference genome, and thus generated |
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69 a tabular file of the mapped reads. You could use this tool to divide the reads |
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70 into those which map onto the genome, and those which don't. |
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71 |
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72 </help> |
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73 </tool> |