Mercurial > repos > peterjc > fastq_filter_by_id
diff tools/fastq/fastq_filter_by_id.xml @ 2:d570cc324779
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:24:08 -0400 |
parents | b79caa511ba2 |
children |
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--- a/tools/fastq/fastq_filter_by_id.xml Tue Jun 07 17:23:49 2011 -0400 +++ b/tools/fastq/fastq_filter_by_id.xml Tue Jun 07 17:24:08 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.3"> +<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.4" hidden="true"> <description>from a tabular file</description> <command interpreter="python"> fastq_filter_by_id.py $input_tabular $columns $input_fastq @@ -54,20 +54,28 @@ </tests> <help> +**Deprecated** + +This tool is now obsolete, and should not be used in future. It has been +replaced by a more general version covering FASTA, FASTQ and SFF in one +single tool. + **What it does** By default it divides a FASTQ file in two, those sequences with or without an ID present in the tabular file column(s) specified. You can opt to have a single output file of just the matching records, or just the non-matching ones. -Note that the order of sequences in the original FASTQ file is preserved. +Note that the order of sequences in the original FASTA file is preserved. Also, if any sequences share an identifier, duplicates are not removed. **Example Usage** -You may have mapped your reads against a reference genome, and thus generated -a tabular file of the mapped reads. You could use this tool to divide the reads -into those which map onto the genome, and those which don't. +You may have performed some kind of contamination search, for example running +BLASTN against a database of cloning vectors or bacteria, giving you a tabular +file containing read identifiers. You could use this tool to extract only the +reads without BLAST matches (i.e. those which do not match your contaminant +database). </help> </tool>