<tool id="protxml_to_gff" name="ProtXML to GFF" version="1.0.1">
	<requirements>
	    <requirement type="package" version="1.3">protk</requirement>
    	<requirement type="package" version="2.2.29">blast+</requirement>	    
   </requirements>

	<description>Map peptides from a protXML file to genomic coordinates</description>

	<command>
		protxml_to_gff.rb -p $protxml_file 

		-g $genome_fasta_file 

		-d $protein_fasta_file 

		-o $output

		--threshold $peptide_threshold

		--prot-threshold $protein_threshold

		$stack_charges

	</command>




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

	<inputs>	
		<param name="protxml_file" type="data" format="protxml" help="ProtXML containing combined results from all searches" label="ProtXML File" />
		<param name="genome_fasta_file" type="data" format="fasta" help="The genome against which peptides will be mapped" label="Genome fasta file" />
		<param name="protein_fasta_file" type="data" format="fasta" help="The database used for ms/ms searches (must have genomic coords encoded in the fasta header)" label="Protein fasta file" />

		<param name="peptide_threshold" help="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" label="Peptide Probability Threshold" />
		<param name="protein_threshold" help="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" label="Protein Probability Threshold" />

		<param name="stack_charges" type="boolean" label="Stack Charges" help="Different peptide charge states get separate gff entries" truevalue="--stack-charge-states" falsevalue=""/>

		<param name="collapse_redundant_proteins" type="boolean" label="Collapse Redundant Proteins" help="Proteins that cover genomic regions already covered will be skipped" truevalue="--collapse-redundant-proteins" falsevalue=""/>

	</inputs>

	<outputs>
		<data format="gff3" name="output" />
	</outputs>


  <help>

**What it does**

Generates a gff file containing genomic coordinates for peptides present in a protXML file.

In order for this tool to work the inputs must satisfy certain requirements. 

1. The genome fasta should encode the scaffold numbers as in the following example

>scaffoldXXX

or 

>scaffold_XXX

where XXX represent digits encoding the scaffold number. Any number of digits are allowed

2. The protXML should have been generated by searching a database generated using the protk Generate 6 frame translation tool and the extract proteins from gff3 tool.  Both those tools should be run with the genomics coordinates included in the output file.



----

**References**


  </help>

</tool>