<tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.3">
	<description>from a tabular file</description>
	<command interpreter="python">
fasta_filter_by_id.py $input_tabular $columns $input_fasta
#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_fasta" type="data" format="fasta" label="FASTA file to filter on the identifiers"/>
		<param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTA identifiers"/>
		<param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA 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 FASTA files</option>
				<option value="pos">Just positive matches (ID on list), as a single FASTA file</option>
				<option value="neg">Just negative matches (ID not on list), as a single FASTA 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="fasta" label="With matched ID">
			<filter>output_choice_cond["output_choice"] != "neg"</filter>
		</data>
		<data name="output_neg" format="fasta" label="Without matched ID">
			<filter>output_choice_cond["output_choice"] != "pos"</filter>
		</data>
	</outputs>
	<tests>
	<!-- Can't get these unit tests to run, may be a Galaxy problem
	<test>
		<param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
		<param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
		<param name="columns" value="1" />
		<param name="output_choice" value="both" />
		<output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
		<output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
	</test>
	<test>
		<param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
		<param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
		<param name="columns" value="1" />
		<param name="output_choice" value="pos" />
		<output name="output_pos" file="four_human_proteins_filter_a.fasta" ftype="fasta" />
	</test>
	<test>
		<param name="input_fasta" value="four_human_proteins.fasta" ftype="fasta" />
		<param name="input_tabular" value="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
		<param name="columns" value="1" />
		<param name="output_choice" value="neg" />
		<output name="output_neg" file="four_human_proteins_filter_b.fasta" ftype="fasta" />
	</test>
	-->
	</tests>
	<help>

**What it does**

By default it divides a FASTA 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**

Given a FASTA file of proteins you might run a signal peptide search (e.g.
via the SignalP wrapper for Galaxy), then filtered these tabular results to
select just those with a signal peptide. You could then use this tool to get
a FASTA file of only the proteins with predicted signal peptides.

	</help>
</tool>