comparison 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

0:10e963c79a45

<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.2">
	<description>from a tabular file</description>
	<command interpreter="python">
fastq_filter_by_id.py $input_tabular $columns $input_fastq
#if $output_choice_cond.output_choice=="both"
 $output_pos $output_neg

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 FASTA file is preserved.
Also, if any sequences share an identifier, duplicates are not removed.

**Example Usage**

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>

1:b79caa511ba2

<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.3">
	<description>from a tabular file</description>
	<command interpreter="python">
fastq_filter_by_id.py $input_tabular $columns $input_fastq
#if $output_choice_cond.output_choice=="both"
 $output_pos $output_neg

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.
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.

	</help>
</tool>