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

--- 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>