<?xml version="1.0"?>

<tool name="MGEScan" id="mgescan" version="0.0.2">
	<description>
		MGEScan
	</description>
	<command interpreter="bash">
		mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 $both_gff3 $mpi_yn.nmpi
		<!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 -->
	</command>
	<inputs>
		<param format="fasta,tabular,data" name="input" type="data" label="Input FASTA file(s)"/>
		<!--param name="hmmver" type="select" label="Hmmsearch version">
			<option selected="selected" value="3">3</option>
			<option value="2">2</option>
		</param-->
		<param name="program" type="select" label="MGEScan">
			<option selected="selected" value="B">Both</option>
			<option value="L">LTR</option>
			<option value="N">nonLTR</option>
		</param>
		<conditional name="mpi_yn">
			<param name="mpi_select" type="select" label="Enable MPI">
				<option value="no_mpi">No</option>
				<option value="yes_mpi">Yes</option>
			</param>
			<when value="yes_mpi">
				<param name="nmpi" format="txt" type="text" value="1" label="Number of MPI Processes"/>
			</when>
			<when value="no_mpi">
				<param name="nmpi" type="hidden" value="0"/>
			</when>
		</conditional>
	</inputs>
	<outputs>
		<data format="ltr.out" name="output" label="LTR Results (ltr.out)">
			<filter>program != "N"</filter>
		</data>
		<data format="fasta" name="clade" label="clade file (FASTA)">
			<filter>program != "L"</filter>
		</data>
		<data format="qfile" name="qvalue_en" label="qvalue_en">
			<filter>program != "L"</filter>
		</data>
		<data format="qfile" name="qvalue_rt" label="qvalue_rt">
			<filter>program != "L"</filter>
		</data>
		<data format="gff3" name="ltr_gff3" label="GFF3 for LTR">
			<filter>program != "N"</filter>
		</data>
		<data format="gff3" name="nonltr_gff3" label="GFF3 for nonLTR">
			<filter>program != "L"</filter>
		</data>
		<data format="gff3" name="both_gff3" label="GFF3 for LTR and nonLTR">
			<filter>program == "B"</filter>
		</data>

	</outputs>
	<help>
How to Run MGEScan
===================

* Select an input genome data from the select box, and choose a program. Both LTR and nonLTR of MGEScan is default.
* Click 'Execute' button.
* MPI will be enabled depending on your system support.

If you like to have more options to run LTR or nonLTR program, use separated tools on the left panel.

For example, in LTR > MGEScan-LTR, preprocessing by repeatmasker and setting other variables are available e.g. distance(bp) between LTRs.

Output
============

A. MGEScan_LTR:

Upon completion, MGEScan-LTR generates a file "ltr.out". This output file has information
about clusters and coordinates of LTR retrotransposons identified. Each cluster of LTR
retrotransposons starts with the head line of "[cluster_number]---------", followed by
the information of LTR retrotransposons in the cluster. The columns for LTR
retrotransposons are as follows.

  1. LTR_id: unique id of LTRs identified. It consist of two components, sequence file name and id in the file. For example, chr1_2 is the second LTR retrotransposon in the chr1 file.
  2. start position of 5’ LTR.
  3. end position of 5’ LTR.
  4. start position of 3’ LTR.
  5. end position of 3’ LTR.
  6. strand: + or -.
  7. length of 5’ LTR.
  8. length of 3’ LTR.
  9. length of the LTR retrotransposon.
  10. TSD on the left side of the LTR retotransposons.
  11. TSD on the right side of the LTR retrotransposons.
  12. di(tri)nucleotide on the left side of 5’LTR
  13. di(tri)nucleotide on the right side of 5’LTR
  14. di(tri)nucleotide on the left side of 3’LTR
  15. di(tri)nucleotide on the right side of 3’LTR 

B. MGEScan_nonLTR:
   Upon completion, MGEScan-nonLTR generates the directory, "info" in the data directory you
   specified. In this "info" directory, two sub-directories ("full" and "validation") are
   generated.

   * The "full" directory is for storing sequences of elements. Each subdirectory in "full"
   is the name of clade. In each directory of clade, the DNA sequences of nonLTRs identified
   are listed. Each sequence is in fasta format. The header contains the position
   information of TEs identified: [genome_file_name]_[start position in the sequence]
 
   For example, >chr1_333 means that this element start at 333bp in the "chr1" file.

   * The "validation" directory is for storing Q values. 
   In the files "en" and "rt", the first column corresponds to the element name and the last column Q value. 

License
============
Copyright 2015.
You may redistribute this software under the terms of the GNU General Public License.

</help>
</tool>