Mercurial > repos > peterjc > fastq_filter_by_id

comparison tools/fastq/fastq_filter_by_id.xml @ 2:d570cc324779

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:24:08 -0400
parents b79caa511ba2
children
comparison
equal deleted inserted replaced
1:b79caa511ba2 2:d570cc324779
1 <tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.3"> 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> 2 <description>from a tabular file</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 fastq_filter_by_id.py $input_tabular $columns $input_fastq 4 fastq_filter_by_id.py $input_tabular $columns $input_fastq
5 #if $output_choice_cond.output_choice=="both" 5 #if $output_choice_cond.output_choice=="both"
6 $output_pos $output_neg 6 $output_pos $output_neg
52 </outputs> 52 </outputs>
53 <tests> 53 <tests>
54 </tests> 54 </tests>
55 <help> 55 <help>
56 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
57 **What it does** 63 **What it does**
58 64
59 By default it divides a FASTQ file in two, those sequences with or without an 65 By default it divides a FASTQ file in two, those sequences with or without an
60 ID present in the tabular file column(s) specified. You can opt to have a 66 ID present in the tabular file column(s) specified. You can opt to have a
61 single output file of just the matching records, or just the non-matching ones. 67 single output file of just the matching records, or just the non-matching ones.
62 68
63 Note that the order of sequences in the original FASTQ file is preserved. 69 Note that the order of sequences in the original FASTA file is preserved.
64 Also, if any sequences share an identifier, duplicates are not removed. 70 Also, if any sequences share an identifier, duplicates are not removed.
65 71
66 **Example Usage** 72 **Example Usage**
67 73
68 You may have mapped your reads against a reference genome, and thus generated 74 You may have performed some kind of contamination search, for example running
69 a tabular file of the mapped reads. You could use this tool to divide the reads 75 BLASTN against a database of cloning vectors or bacteria, giving you a tabular
70 into those which map onto the genome, and those which don't. 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).
71 79
72 </help> 80 </help>
73 </tool> 81 </tool>