Mercurial > repos > peterjc > fastq_filter_by_id
comparison tools/fastq/fastq_filter_by_id.xml @ 3:e0041942a12d draft default tip
v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author | peterjc |
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date | Fri, 03 Feb 2017 05:34:18 -0500 |
parents | d570cc324779 |
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2:d570cc324779 | 3:e0041942a12d |
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1 <tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.4" hidden="true"> | |
2 <description>from a tabular file</description> | |
3 <command interpreter="python"> | |
4 fastq_filter_by_id.py $input_tabular $columns $input_fastq | |
5 #if $output_choice_cond.output_choice=="both" | |
6 $output_pos $output_neg | |
7 #elif $output_choice_cond.output_choice=="pos" | |
8 $output_pos - | |
9 #elif $output_choice_cond.output_choice=="neg" | |
10 - $output_neg | |
11 #end if | |
12 </command> | |
13 <inputs> | |
14 <param name="input_fastq" type="data" format="fastq" label="FASTQ file to filter on the identifiers"/> | |
15 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTQ identifiers"/> | |
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"> | |
17 <validator type="no_options" message="Pick at least one column"/> | |
18 </param> | |
19 <conditional name="output_choice_cond"> | |
20 <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> | |
21 <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two FASTA files</option> | |
22 <option value="pos">Just positive matches (ID on list), as a single FASTA file</option> | |
23 <option value="neg">Just negative matches (ID not on list), as a single FASTA file</option> | |
24 </param> | |
25 <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> | |
26 <when value="both" /> | |
27 <when value="pos" /> | |
28 <when value="neg" /> | |
29 </conditional> | |
30 </inputs> | |
31 <outputs> | |
32 <data name="output_pos" format="fastq" label="With matched ID"> | |
33 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
34 <change_format> | |
35 <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
36 <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
37 <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
38 <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
39 </change_format> | |
40 <filter>output_choice_cond["output_choice"] != "neg"</filter> | |
41 </data> | |
42 <data name="output_neg" format="fastq" label="Without matched ID"> | |
43 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
44 <change_format> | |
45 <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
46 <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
47 <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
48 <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
49 </change_format> | |
50 <filter>output_choice_cond["output_choice"] != "pos"</filter> | |
51 </data> | |
52 </outputs> | |
53 <tests> | |
54 </tests> | |
55 <help> | |
56 | |
57 **Deprecated** | |
58 | |
59 This tool is now obsolete, and should not be used in future. It has been | |
60 replaced by a more general version covering FASTA, FASTQ and SFF in one | |
61 single tool. | |
62 | |
63 **What it does** | |
64 | |
65 By default it divides a FASTQ file in two, those sequences with or without an | |
66 ID present in the tabular file column(s) specified. You can opt to have a | |
67 single output file of just the matching records, or just the non-matching ones. | |
68 | |
69 Note that the order of sequences in the original FASTA file is preserved. | |
70 Also, if any sequences share an identifier, duplicates are not removed. | |
71 | |
72 **Example Usage** | |
73 | |
74 You may have performed some kind of contamination search, for example running | |
75 BLASTN against a database of cloning vectors or bacteria, giving you a tabular | |
76 file containing read identifiers. You could use this tool to extract only the | |
77 reads without BLAST matches (i.e. those which do not match your contaminant | |
78 database). | |
79 | |
80 </help> | |
81 </tool> |