annotate tools/fastq/fastq_paired_unpaired.xml @ 0:72e9fcaec61f

Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository

<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.0.4">
	<description>using the read name suffices</description>
	<command interpreter="python">
fastq_paired_unpaired.py $input_fastq.extension $input_fastq
#if $output_choice_cond.output_choice=="separate"
 $output_forward $output_reverse
#elif $output_choice_cond.output_choice=="interleaved"
 $output_paired
#end if
$output_singles
	</command>
	<inputs>
		<param name="input_fastq" type="data" format="fastq" label="FASTQ file to divide into paired and unpaired reads"/>
		<conditional name="output_choice_cond">
			<param name="output_choice" type="select" label="How to output paired reads?">
				<option value="separate">Separate (two FASTQ files, for the forward and reverse reads, in matching order).</option>
				<option value="interleaved">Interleaved (one FASTQ file, alternating forward read then partner reverse read).</option>
			</param>
			<!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
			<when value="separate" />
			<when value="interleaved" />
		</conditional>
	</inputs>
	<outputs>
		<data name="output_singles" format="input" label="Orphan or single reads"/>
		<data name="output_forward" format="input" label="Forward paired reads">
			<filter>output_choice_cond["output_choice"] == "separate"</filter>
		</data>
		<data name="output_reverse" format="input" label="Reverse paired reads">
			<filter>output_choice_cond["output_choice"] == "separate"</filter>
		</data>
		<data name="output_paired" format="input" label="Interleaved paired reads">
			<filter>output_choice_cond["output_choice"] == "interleaved"</filter>
		</data>
	</outputs>
	<tests>
	</tests>
	<requirements>
		<requirement type="python-module">Bio</requirement>
	</requirements>
	<help>

**What it does**

Using the common read name suffix conventions, it divides a FASTQ file into
paired reads, and orphan or single reads.

The input file should be a valid FASTQ file which has been sorted so that
any partner forward+reverse reads are consecutive. The output files all
preserve this sort order. Pairing are recognised based on standard name
suffices. See below or run the tool with no arguments for more details.

Any reads where the forward/reverse naming suffix used is not recognised
are treated as orphan reads. The tool supports the /1 and /2 convention
used by Illumina, the .f and .r convention, and the Sanger convention
(see http://staden.sourceforge.net/manual/pregap4_unix_50.html for details).

Note that this does support multiple forward and reverse reads per template
(which is quite common with Sanger sequencing), e.g. this which is sorted
alphabetically:

WTSI_1055_4p17.p1kapIBF
WTSI_1055_4p17.p1kpIBF
WTSI_1055_4p17.q1kapIBR
WTSI_1055_4p17.q1kpIBR

or this where the reads already come in pairs:

WTSI_1055_4p17.p1kapIBF
WTSI_1055_4p17.q1kapIBR
WTSI_1055_4p17.p1kpIBF
WTSI_1055_4p17.q1kpIBR

both become:

WTSI_1055_4p17.p1kapIBF paired with WTSI_1055_4p17.q1kapIBR
WTSI_1055_4p17.p1kpIBF paired with WTSI_1055_4p17.q1kpIBR

	</help>
</tool>