annotate tools/filters/sff_filter_by_id.xml @ 1:9cd3591f6afa default tip

Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository

<tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.2" hidden="true">
	<description>from a tabular file</description>
	<command interpreter="python">
sff_filter_by_id.py $input_tabular $columns $input_sff
#if $output_choice_cond.output_choice=="both"
 $output_pos $output_neg
#elif $output_choice_cond.output_choice=="pos"
 $output_pos -
#elif $output_choice_cond.output_choice=="neg"
 - $output_neg
#end if
	</command>
	<inputs>
		<param name="input_sff" type="data" format="sff" label="SFF file to filter on the identifiers"/>
		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing SFF identifiers"/>
		<param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing SFF identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns">
			<validator type="no_options" message="Pick at least one column"/>
		</param>
		<conditional name="output_choice_cond">
			<param name="output_choice" type="select" label="Output positive matches, negative matches, or both?">
				<option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two SFF files</option>
				<option value="pos">Just positive matches (ID on list), as a single SFF file</option>
				<option value="neg">Just negative matches (ID not on list), as a single SFF file</option>
			</param>
			<!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
			<when value="both" />
			<when value="pos" />
			<when value="neg" />
		</conditional>
	</inputs>
	<outputs>
		<data name="output_pos" format="sff" label="With matched ID">
			<filter>output_choice_cond["output_choice"] != "neg"</filter>
		</data>
		<data name="output_neg" format="sff" label="Without matched ID">
			<filter>output_choice_cond["output_choice"] != "pos"</filter>
		</data>
	</outputs>
	<tests>
	</tests>
	<requirements>
		<requirement type="python-module">Bio</requirement>
	</requirements>
	<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 It has been
replaced by a more general version covering FASTA, FASTQ and SFF in one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 Standard Flowgram Format (SFF) 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 SFF file is preserved, as is
any Roche XML Manifest. Also, if any sequences share an identifier (which would
be very unusual in SFF files, 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).

**Citation**

This tool uses Biopython to read and write SFF files. If you use this tool in
scientific work leading to a publication, please cite the Biopython application
note:

Cock et al 2009. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

	</help>
</tool>