<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.0">
	<requirements>
		<container type="docker">iracooke/protk-1.4.1</container>
	    <requirement type="package" version="1.4">protk</requirement>
   </requirements>

	<description>
		Generate random protein sequences with the same AA composition as input sequences
	</description>

	<command>
		make_decoy.rb $fasta_file -o $output -P $prefix_string $append
	</command>

	<stdio>
		<exit_code range="1:"   level="fatal"   description="Failure" />
	</stdio>

	<inputs>	
		<param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
		<param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>		
		<param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
	</inputs>

	<outputs>
		<data format="fasta" name="output" />
	</outputs>

	<tests>
	  <test>
	      <param name="fasta_file" value="testdb.fasta" format="fasta"/>
	      <output name="output" format="fasta">
	      	<assert_contents>
	      	    <has_text text="decoy_rp3" />
	      	</assert_contents>
	      </output>
	  </test>
	</tests>



  <help>

**What it does**

Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches


  </help>

</tool>