--- a/mgescan.xml	Mon Feb 15 01:50:27 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-<?xml version="1.0"?>
-
-<tool name="MGEScan" id="mgescan" version="0.0.2">
-	<description>
-		MGEScan
-	</description>
-	<requirements>
-	<requirement type="package" version="3.0">mgescan</requirement>
-	</requirements>
-	<version_command>mgescan --version</version_command>
-	<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>