<tool id="GenePhys" name="GenePhys" version="1.1.1">
<description>Extract the genes underlying a genetic segment defined by genetic markers</description>
<command interpreter="perl">

  #if $extractseq.do_extractseq=="YES"
      GenePhys.pl -extractseq $extractseq.do_extractseq -input_assembly_file $input_assembly_file -input_markers_position_file $input_markers_position_file -input_markers_file $input_markers_file -window $window -offset $offset -output_segment_file $output_segment_file -output_fasta_file $output_fasta_file -log_file $log_file -input_blast_files $input_blast_files -max_blast_lines $max_blast_lines -input_genes_position_file $input_genes_position_file -output_genes_list_file $output_genes_list_file
  #else
      GenePhys.pl -input_markers_position_file $input_markers_position_file -input_markers_file $input_markers_file -window $window -offset $offset -output_segment_file $output_segment_file -output_fasta_file $output_fasta_file -log_file $log_file -input_blast_files $input_blast_files -max_blast_lines $max_blast_lines -input_genes_position_file $input_genes_position_file -output_genes_list_file $output_genes_list_file
  #end if



    
</command>
<inputs>
	<param name="input_markers_file"  type="data" format="txt" label="Select a suitable input MARKERS file from your history"/>
	<param name="input_markers_position_file"  type="data" format="txt" label="Select a suitable input MARKERS POSITION file from your history"/>
	<param name="input_genes_position_file"  type="data" format="txt" label="Select a suitable input GENE POSITION file from your history"/>
	<param name="input_blast_files"  type="data" format="txt" multiple="true" label="Select a BLAST files from your history"/>
	<param name="window" type="integer" value="200000" label="Maximum distance between markers of a segment (Threshold for splitting a segment)"/>
	<param name="offset" type="integer" value="100000" label="Additionnal segment size in 5' and 3' (security marging)"/>
	<param name="max_blast_lines"  type="integer" value="3" label="Select the maximum number of BLAST best match to show"/>

	<conditional name="extractseq">
  		<param name="do_extractseq" type="select" label="Extract genomic segment">
    			<option value="NO">NO</option>
    			<option value="YES">YES</option>
  		</param>
  		<when value="YES">
    			<param name="input_assembly_file"  type="data" format="fasta" label="Select a suitable input ASSEMBLY file from your history"/>
  		</when>
  		<when value="NO"></when>
	</conditional> 

</inputs>
<outputs>
	<data name="output_segment_file" format="txt" label="SEGMENT ${tool.name} on ${on_string}"/>
	<data name="output_fasta_file" format="fasta" label="FASTA ${tool.name} on ${on_string}"/>
	<data name="output_genes_list_file" format="txt" label="GENES ${tool.name} on ${on_string}"/>
	<data name="log_file" format="txt" label="LOG ${tool.name} on ${on_string}"/>
</outputs>

<help>



</help>
</tool>