<tool id="cut_degen" name="Cut degenerate primers from dataset (for Fastq)" version="0.1.0">
	<description> Degenerate primer removal tool for Fastq files</description>
    <requirements>
	<requirement type = "package" version = "1.9">numpy</requirement>
	<requirement type = "package" version = "1.65">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="python">cut_degen.py $input1 $input2 $input3 $input4 $input5 $input6
    </command>
    <inputs>
	<param name="input1" type="data" label="Input Fastq file" help="Please add a valid Fastq file!" format="fastq"/>
	<param name="input2" type="text" label="Input adaptor" help="This will work also with degenerate adaptors. Type the adaptor here..." size="4x25" area="true"/>
	<param name="input3" type="select" label="Keep reads without adaptor?" help="This is a True/False option, if True, reads that lack the adaptor will be kept. If false, they will be deleted from the dataset.">
			<option value="True">True</option>
			<option value="False">False</option>
		</param>
	<param name="input4" type="select" label = "Remove adaptors?" help="This is True/False option, if True, removes adaptors from sequences. If false, keeps the adaptors in the sequences.">
			<option value="True">True</option>
			<option value="False">False</option>
		</param>
	<param name="input5" type="select" multiple="False" label="5' or 3' end" help="Enter '5' to remove the primer from the 5' end, and enter '3' to remove the primer from the 3' end">
        <option value="5">5</option>
		<option value="3">3</option>
        </param>
        <param name="input6" type="text" label="Adaptor name" help="Enter an identifier for your adaptor to be recorded in the output .txt file" size="4x25" area="true">
		</param>
    </inputs>
	<outputs>
		<data name="output1" format="text" from_work_dir="output.txt" label="Degenerate adaptor removal on ${input1.name}(REPORT)"/>
		<data name="output2" format="fastq" from_work_dir="output.fastq" label="Degenerate adaptor removal on ${input1.name}(READS)"/>
    </outputs>
	<tests>
			<test>
	<param name="input1" value="test.fastq"/>
	<param name="input2"  value="ACCTGCCTGCCG"/>
	<param name="input3" value="True"/>
	<param name="input4" value="True"/>
	<param name="input5" value="5"/>
    <param name="input6"  value="UniA"/>
	<output name="output1" file="output.txt"/>
	<output name="output2" file="output.fastq"/>
        </test>
		<test>
			<param name="input1" value="test3prime.fastq"/>
			<param name="input2" value="GCTCGGTGGCGT"/>
			<param name="input3" value="True"/>
			<param name="input4" value="True"/>
			<param name="input5" value="3"/>
			<param name="input6" value="UniB"/>
			<output name="output1" file="output2.txt"/>
			<output name="output2" file="output2.fastq"/>
		</test>
    </tests>
    <help>
This program takes Fastq files and removes a given degenerate primer sequence. There are a few arguments that you can put in:
        1) You can check whether or not to keep reads that do not have the adaptor in it.
        2) You can check whether or not to remove the adaptor sequences from your reads.
        3) You can choose whether to cut adaptors from the 5', or 3' end of the molecules.
		4) You can add an identifier for the adaptor which will show up in the output text file.

    </help>
	<citations>
	<citation type="doi">10.1093/bioinformatics/btp163</citation>
	</citations>
</tool>