--- a/mgescan.xml	Sat Jun 14 19:00:14 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-<?xml version="1.0"?>
-
-<tool name="MGEScan" id="mgescan" version="0.0.1" workflow_compatible="false">
-	<description>
-		MGEScan
-	</description>
-	<command interpreter="bash">
-		mgescan.sh $input '$input.name' 3 $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3
-		<!-- mgescan.sh $input $input.name $hmmver $output $program $clade $qvalue_en $qvalue_rt $ltr_gff3 $nonltr_gff3 -->
-	</command>
-	<inputs>
-		<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-->
-		<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>
-	</inputs>
-	<outputs>
-		<data format="ltr.out" name="output">
-			<filter>program != "N"</filter>
-		</data>
-		<data format="fasta" name="clade">
-			<filter>program != "L"</filter>
-		</data>
-		<data format="qfile" name="qvalue_en">
-			<filter>program != "L"</filter>
-		</data>
-		<data format="qfile" name="qvalue_rt">
-			<filter>program != "L"</filter>
-		</data>
-		<data format="gff3" name="ltr_gff3">
-			<filter>program != "N"</filter>
-		</data>
-		<data format="gff3" name="nonltr_gff3">
-			<filter>program != "L"</filter>
-		</data>
-
-	</outputs>
-	<help>
-Running the program
-===================
-
-To run MGEScan, select input genome data in From select box, and select program either LTR, nonLTR or both.
-
-Click 'Execute' button.
-
-If you like to have more options to run LTR or nonLTR progrma, use separated tools on the left panel.
-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 2014 Mina Rho, Haixu Tang.
-You may redistribute this software under the terms of the GNU General Public License.
-
-</help>
-</tool>