<?xml version="1.0"?>

<tool name="MGEScan-LTR" id="mgescan-ltr" version="0.0.1" workflow_compatible="false">
	<description>
		de novo identification of LTR retroelements
	</description>
	<!--
	<action module="galaxy.tools.actions.nonltr" class="nonltrToolAction"/>
	<requirements>
		<requirement type="package">HMMER</requirement>
		<requirement type="package">EMBOSS</requirement>
	</requirements>
	-->
	<command interpreter="bash">
		<!--
		/u/lee212/retrotminer/MGEScan_LTR/find_ltr.pl -genome=/u/lee212/retrotminer/MGEScan_nonLTR_v2/anoGam1/ 
		-data=/u/lee212/retrotminer/MGEScan_LTR/example/data/  -program=/u/lee212/retrotminer/MGEScan_LTR/
		-->
		<!--mgescan.sh $input $input.name $hmmver $output L None None None $ltr_gff3 None-->
		<!--mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None-->
		mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
	</command>
	<inputs>
		<!--
		<param name="genome" type="text" label="directory where input genome data exists" />
		<param name="data" type="text" label="directory of the output" />
		-->
		<param format="txt" name="input" type="data" label="From"/>
		<!--param name="hmmver" type="select" label="Hmmsearch version">
			<option selected="selected" value="3">3</option>
			<option value="2">2</option>
		</param-->
		<!-- path.conf -->
		<param name="sw_rm" type="select" display="checkboxes" multiple="True" label="enable repeatmasker, if necessary" help="Use this option if you are enable repeatmasker"> 
			<option value="Yes">Yes</option>
		</param>
		<param name="scaffold" type="text" label="path for the big file that has all scaffolds"/>
		<!-- value.conf -->
		<param name="min_dist" type="text" value="2000" label="minimum distance(bp) between LTRs" />
		<param name="max_dist" type="text" value="20000" label="maximum distance(bp) between LTRs" />
		<param name="min_len_ltr" type="text" value="130" label="minimum length(bp) of LTR"/>
		<param name="max_len_ltr" type="text" value="2000" label="maximum length(bp) of LTR"/>
		<param name="ltr_sim_condition" type="text" value="70" label="minimum similarity(%) for LTRs in an element"/>
		<param name="cluster_sim_condition" type="text" value="70" label="inimum similarity(%) for LTRs in a cluster"/>
		<param name="len_condition" type="text" value="70" label="minimum length(bp) for LTRs aligned in local alignment"/>
	</inputs>
	<outputs>
		<data format="ltr.out" name="output" />
		<data format="gff3" name="ltr_gff3" />
		<data format="repeatmasker" name="repeatmasker" >
			<filter>sw_rm == "Yes"</filter>
		</data>
	</outputs>
	<help>
Running the program
===================

To run MGEScan-LTR, follow the steps below,

1. Specify options that you like to have:

   * Check repeatmasker if you want to preprocess
   * Check scaffold if the input file has all scaffolds.

2. Update values:

   * min_dist: minimum distance(bp) between LTRs.
   * max_dist: maximum distance(bp) between LTRS
   * min_len_ltr: minimum length(bp) of LTR.
   * max_len_ltr: maximum length(bp) of LTR.
   * ltr_sim_condition: minimum similarity(%) for LTRs in an element.
   * cluster_sim_condition: minimum similarity(%) for LTRs in a cluster
   * len_condition: minimum length(bp) for LTRs aligned in local alignment.

4. Click 'Execute'

   * mask known repeats other than LTR retrotransposons
   * identify LTRs

Output
======

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 5LTR
13. di(tri)nucleotide on the right side of 5LTR
14. di(tri)nucleotide on the left side of 3LTR
15. di(tri)nucleotide on the right side of 3LTR 

License
============

Copyright 2014 Mina Rho, Haixu Tang.
You may redistribute this software under the terms of the GNU General Public License.
</help>
</tool>