# HG changeset patch
# User bjoern-gruening
# Date 1359707377 18000
# Node ID f8f1a3878edd1a0672bb01176009e3f487d2cb28
# Parent  13df908a02b0b4b33a90b98ed8b265eb77e7c277
0.1.1 version, prevent a crash if no repeat is found. Thanks to Simon Guest

diff -r 13df908a02b0 -r f8f1a3878edd RepeatMasker.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RepeatMasker.xml	Fri Feb 01 03:29:37 2013 -0500
@@ -0,0 +1,314 @@
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="0.1.1">
+    <description>Masks different kind of repeats</description>
+    <command>
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+
+## create temp directory
+#import tempfile, os
+#set $dirname = os.path.abspath(tempfile.mkdtemp())
+#set $input_filename = os.path.split(str($query))[-1]
+#set $output_basename = os.path.join($dirname, $input_filename)
+
+
+RepeatMasker 
+-parallel 8
+
+$nolow
+$noint
+$norna
+
+#if str($species)!="all":
+    $species
+#end if
+
+
+-dir $dirname
+
+#if $adv_opts.adv_opts_selector=="advanced":
+
+    #if str($adv_opts.gc)!="0":
+        -gc $adv_opts.gc
+    #end if
+
+    $adv_opts.gccalc
+
+    #set $output_files_list = str($adv_opts.output_files).split(',')
+    #if "gff" in $output_files_list:
+        -gff
+    #end if
+    #if "html" in $output_files_list:
+        -html
+    #end if
+
+    $adv_opts.slow_search
+    $adv_opts.quick_search
+    $adv_opts.rush_search
+    $adv_opts.only_alus
+    $adv_opts.is_only
+
+#else:
+    ## Set defaults
+    -gff
+
+## End of advanced options:
+#end if
+
+$query
+
+
+> /dev/null 2> /dev/null;
+## Copy the output files to galaxy
+## AgR: if there are no repeats, the output files may not exist.
+## This causes the job to fail, so touch files to ensure they exist.
+#if $adv_opts.adv_opts_selector=="advanced":
+
+    #if "summary" in $output_files_list:
+        ## Write out the summary file (default)
+        #set $summary_file = $output_basename + '.tbl'
+        touch $summary_file
+        cp $summary_file $output_summary;
+    #end if
+
+    #if "gff" in $output_files_list:
+        ## Write out the gff file (default)
+        #set $gff_file = $output_basename + '.out.gff'
+        touch $gff_file
+        cp $gff_file $output_gff;
+    #end if
+
+    #if "html" in $output_files_list:
+        ## Write out the html file
+        #set $html_file = $output_basename + '.out.html'
+        touch $html_file
+        cp $html_file $output_html;
+    #end if
+
+#else:
+
+    ## Write out the summary file (default)
+    #set $summary_file = $output_basename + '.tbl'
+    touch $summary_file
+    cp $summary_file $output_summary;
+
+    ## Write out the gff file (default)
+    #set $gff_file = $output_basename + '.out.gff'
+    touch $gff_file
+    cp $gff_file $output_gff;
+
+
+## End of advanced options:
+#end if
+
+## Write out mask sequence file
+#set $mask_sequence_file = $output_basename + '.masked'
+touch $mask_sequence_file
+cp $mask_sequence_file $output_mask;
+
+## Write out standard file (default)
+## The default '.out' file from RepeatMasker has a 3-line header and spaces rather
+## than tabs. Remove the header and replace the whitespaces with tab
+#set $standard_file = $output_basename + '.out'
+tail -n +4 $standard_file | tr -s ' ' '\t' > $output_std;
+
+## Delete all temporary files
+rm $dirname -r;
+
+
+    </command>
+    <inputs>
+        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+
+        <param name="nolow" type="boolean" label="No low complexity DNA" truevalue="-nolow" falsevalue="" checked="false" help="Does not mask low_complexity DNA or simple repeats."/>
+        <param name="noint" type="boolean" label="No interspersed repeats" truevalue="-noint" falsevalue="" checked="false" help="Only masks low complex/simple repeats (no interspersed repeats)."/>
+
+        <param name="norna" type="boolean" label="No small RNA genes" truevalue="-norna" falsevalue="" checked="false" help="Does not mask small RNA (pseudo) genes."/>
+
+        <!--
+            Specify the species or clade of the input sequence. The species name
+            must be a valid NCBI Taxonomy Database species name and be contained
+            in the RepeatMasker repeat database. The following collection is not complete.
+        -->
+        <param name="species" type="select" label="Species" help="The list is not complete, if you need other species contact your administrator.">
+            <option value="-species anopheles">anopheles</option>
+            <option value="-species arabidopsis">arabidopsis</option>
+            <option value="-species artiodactyl">artiodactyl</option>
+            <option value="-species aspergillus">aspergillus</option>
+            <option value="-species carnivore">carnivore</option>
+            <option value="-species cat">cat</option>
+            <option value="-species chicken">chicken</option>
+            <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
+            <option value="-species 'ciona savignyi'">ciona savignyi</option>
+            <option value="-species cow">cow</option>
+            <option value="-species danio">danio</option>
+            <option value="-species diatoaea">diatoaea</option>
+            <option value="-species dog">dog</option>
+            <option value="-species drosophila">drosophila</option>
+            <option value="-species elegans">elegans</option>
+            <option value="-species fugu">fugu</option>
+            <option value="-species fungi" selected="true">fungi</option>
+            <option value="-species human">human</option>
+            <option value="-species maize">maize</option>
+            <option value="-species mammal">mammal</option>
+            <option value="-species mouse">mouse</option>
+            <option value="-species pig">pig</option>
+            <option value="-species rat">rat</option>
+            <option value="-species rice">rice</option>
+            <option value="-species rodentia">rodentia</option>
+            <option value="-species wheat">wheat</option>
+        </param>
+
+        <conditional name="adv_opts">
+            <param name="adv_opts_selector" type="select" label="Advanced Options">
+              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="advanced">Show Advanced Options</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
+
+
+              <param name="is_only" type="boolean" label="Mask only E coli insertion elements" truevalue="-is_only" falsevalue="" checked="false" help="Only clips E coli insertion elements out of fasta and .qual files."/>
+
+
+              <param name="slow_search" type="boolean" label="Slow search" truevalue="-s" falsevalue="" checked="false" help="0-5% more sensitive, 2-3 times slower than default."/>
+              <param name="quick_search" type="boolean" label="Quick search" truevalue="-q" falsevalue="" checked="false" help="5-10% less sensitive, 2-5 times faster than default."/>
+              <param name="rush_search" type="boolean" label="Rush search" truevalue="-qq" falsevalue="" checked="false" help="about 10% less sensitive, 4->10 times faster than default."/>
+
+              <param name="only_alus" type="boolean" label="Only Alus" truevalue="-alu" falsevalue="" checked="false" help="Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)."/>
+
+              <param name="gccalc" type="boolean" label="Use GC depended matrices, automaticly" truevalue="-gccalc" falsevalue="" checked="true" help="RepeatMasker calculates the GC content even for batch files/small seqs"/>
+
+              <param name="output_files" type="select" multiple="true" label="Additional output files">
+                  <option selected="true" value="summary">Summary file</option>
+                  <option value="gff">GFF file</option>
+                  <option value="html">HTML file</option>
+                  <option value="mask">Mask FastA file</option>
+              </param>
+
+
+              <param name="gc" type="integer" value="0" label="Use GC depended matrices" help="Use matrices calculated for 'number' percentage background GC level">
+                    <validator type="in_range" min="0" />
+                    <validator type="in_range" max="100" />
+              </param>
+
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="output_std" format="tabular" label="${tool.name} on ${on_string}: Standard" />
+        <data name="output_mask" format="fasta" label="${tool.name} on ${on_string}: Mask sequence">
+            <filter>
+                    (adv_opts['adv_opts_selector'] == 'advanced' and 'mask' in adv_opts['output_files'])
+            </filter>
+        </data>
+        <data name="output_summary" format="txt" label="${tool.name} on ${on_string}: Summary">
+            <filter>(
+                    (adv_opts['adv_opts_selector'] == 'advanced' and 'summary' in adv_opts['output_files'])
+                    or
+                    (adv_opts['adv_opts_selector'] == 'basic')
+                    )
+            </filter>
+        </data>
+        <data name="output_html" format="html" label="${tool.name} on ${on_string}: HTML">
+            <filter>(adv_opts['adv_opts_selector'] == 'advanced' and 'html' in adv_opts['output_files'])</filter>
+        </data>
+        <data name="output_gff" format="gff" label="${tool.name} on ${on_string}: GFF">
+            <filter>
+                    (adv_opts['adv_opts_selector'] == 'advanced' and 'gff' in adv_opts['output_files'])
+            </filter>
+        </data>
+    </outputs>
+    <requirements>
+        <requirement type="binary">RepeatMasker</requirement>
+    </requirements>
+    <help>
+    
+.. class:: warningmark
+
+**What it does**
+
+RepeatMasker is a program that screens DNA sequences for *interspersed repeats*
+and *low complexity* DNA sequences. The output of the program is a detailed
+annotation of the repeats that are present in the query sequence as well as a
+modified version of the query sequence in which all the annotated repeats have
+been masked (default: replaced by Ns).
+
+-----
+
+**How to read the results**
+
+
+
+The annotation file contains the cross_match output lines. It lists all best matches
+(above a set minimum score) between the query sequence and any of the sequences in
+the repeat database or with low complexity DNA. The term "best matches" reflects
+that a match is not shown if its domain is over 80% contained within the domain
+of a higher scoring match, where the "domain" of a match is the region in
+the query sequence that is defined by the alignment start and stop. These domains
+have been masked in the returned masked sequence file. In the output, matches are
+ordered by query name, and for each query by position of the start of the alignment.
+
+Example:
+
+======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
+SW score perc div. perc del. perc ins. query seq. q-pos begin q-pos end (left)    w complement matching repeat repeat class/family repeat-pos begin repeat-pos end (left)  ID
+======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
+    1306 15.6      6.2       0.0       HSU08988   6563        6781      \(22462)  C            MER7A           DNA/MER2_type       336              103            \(0)    1
+   12204 10.0      2.4       1.8       HSU08988   6782        7714      \(21529)  C            TIGGER1         DNA/MER2_type       2418             1493           \(0)    2
+     279  3.0      0.0       0.0       HSU08988   7719        7751      \(21492)  +            (TTTTA)n        Simple_repeat       1                33             \(0)    3
+    1765 13.4      6.5       1.8       HSU08988   7752        8022      \(21221)  C            AluSx           SINE/Alu            289              1              \(23)   4
+   12204 10.0      2.4       1.8       HSU08988   8023        8694      \(20549)  C            TIGGER1         DNA/MER2_type       1493             827            \(925)  5
+    1984 11.1      0.3       0.7       HSU08988   8695        9000      \(20243)  C            AluSg           SINE/Alu            305              1              \(5)    6
+   12204 10.0      2.4       1.8       HSU08988   9001        9695      \(19548)  C            TIGGER1         DNA/MER2_type       827              2              \(1591) 7
+     711 21.2      1.4       0.0       HSU08988   9696        9816      \(19427)  C            MER7A           DNA/MER2_type       122              2              \(224)  8
+======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
+
+This is a sequence in which a Tigger1 DNA transposon has integrated into a MER7 DNA transposon copy.
+Subsequently two Alus integrated in the Tigger1 sequence. The simple repeat is derived from the
+poly A of the Alu element. The first line is interpreted like this:
+
+:Table description:
+
+1. **1306** = Smith-Waterman score of the match, usually complexity adjusted
+        The SW scores are not always directly comparable. Sometimes
+        the complexity adjustment has been turned off, and a variety of
+        scoring-matrices are used.
+
+#. **15.6** = % substitutions in matching region compared to the consensus
+#. **6.2** = % of bases opposite a gap in the query sequence (deleted bp)
+#. **0.0** = % of bases opposite a gap in the repeat consensus (inserted bp)
+#. **HSU08988** = name of query sequence
+#. **6563** = starting position of match in query sequence
+#. **7714** = ending position of match in query sequence
+#. **(22462)** = no. of bases in query sequence past the ending position of match
+#. **C**       = match is with the Complement of the consensus sequence in the database
+#. **MER7A**   = name of the matching interspersed repeat
+#. **DNA/MER2_type** = the class of the repeat, in this case a DNA transposon fossil of the MER2 group (see below for list and references)
+#. **2418**    = starting position of match in database sequence (using top-strand numbering)
+#. **1465**    = ending position of match in database sequence
+#. **(0)**     = no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match (so 0 means that the match extended all the way to the end of the repeat consensus sequence)
+#. **1**    = Identifier
+
+An asterisk (\*) in the final column (no example shown) indicates that there is
+a higher-scoring match whose domain partly (&lt;80%) includes the domain of this match. 
+
+Note that the SW score and divergence numbers for the three Tigger1 lines are identical.
+This is because the information is derived from a single alignment (the Alus were deleted
+from the query before the alignment with the Tigger element was performed).
+The program makes educated guesses about many fragments if they are derived from
+the same element (e.g. it knows that the MER7A fragments represent one insert).
+In a next version I can identify each element with a unique ID, if interest exists
+(this could help to represent repeats cleaner in graphic displays). 
+
+
+-------
+
+**References**
+
+Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
+
+http://www.repeatmasker.org/
+
+    </help>
+</tool>
diff -r 13df908a02b0 -r f8f1a3878edd readme.txt
--- a/readme.txt	Wed Jan 11 04:50:59 2012 -0500
+++ b/readme.txt	Fri Feb 01 03:29:37 2013 -0500
@@ -1,7 +1,7 @@
 Galaxy wrapper for RepeatMasker
 =====================================
 
-This wrapper is copyright 2012 by Björn Grüning.
+This wrapper is copyright 2013 by Björn Grüning.
 
 This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology.
 http://www.repeatmasker.org/
@@ -34,6 +34,7 @@
 =======
 
 v0.1 - Initial public release
+v0.1.1 - patch from Simon Guest, to create empty files if no repeat is found
 
 
 Wrapper Licence (MIT/BSD style)
diff -r 13df908a02b0 -r f8f1a3878edd tools/RepeatMasker.xml
--- a/tools/RepeatMasker.xml	Wed Jan 11 04:50:59 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,309 +0,0 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="0.1">
-    <description>Masks different kind of repeats</description>
-    <command>
-## The command is a Cheetah template which allows some Python based syntax.
-## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
-
-## create temp directory
-#import tempfile, os
-#set $dirname = os.path.abspath(tempfile.mkdtemp())
-#set $input_filename = os.path.split(str($query))[-1]
-#set $output_basename = os.path.join($dirname, $input_filename)
-
-
-RepeatMasker 
--parallel 8
-
-$nolow
-$noint
-$norna
-
-#if str($species)!="all":
-    $species
-#end if
-
-
--dir $dirname
-
-#if $adv_opts.adv_opts_selector=="advanced":
-
-    #if str($adv_opts.gc)!="0":
-        -gc $adv_opts.gc
-    #end if
-
-    $adv_opts.gccalc
-
-    #set $output_files_list = str($adv_opts.output_files).split(',')
-    #if "gff" in $output_files_list:
-        -gff
-    #end if
-    #if "html" in $output_files_list:
-        -html
-    #end if
-
-    $adv_opts.slow_search
-    $adv_opts.quick_search
-    $adv_opts.rush_search
-    $adv_opts.only_alus
-    $adv_opts.is_only
-
-#else:
-    ## Set defaults
-    -gff
-
-## End of advanced options:
-#end if
-
-$query
-
-
-> /dev/null 2> /dev/null;
-## Copy the output files to galaxy
-#if $adv_opts.adv_opts_selector=="advanced":
-
-    #if "summary" in $output_files_list:
-        ## Write out the summary file (default)
-        #set $summary_file = $output_basename + '.tbl'
-        cp $summary_file $output_summary;
-    #end if
-
-    #if "gff" in $output_files_list:
-        ## Write out the gff file (default)
-        #set $gff_file = $output_basename + '.out.gff'
-        cp $gff_file $output_gff;
-    #end if
-
-    #if "html" in $output_files_list:
-        ## Write out the html file
-        #set $html_file = $output_basename + '.out.html'
-        cp $html_file $output_html;
-    #end if
-
-#else:
-
-    ## Write out the summary file (default)
-    #set $summary_file = $output_basename + '.tbl'
-    cp $summary_file $output_summary;
-
-    ## Write out the gff file (default)
-    #set $gff_file = $output_basename + '.out.gff'
-    cp $gff_file $output_gff;
-
-
-## End of advanced options:
-#end if
-
-## Write out mask sequence file
-#set $mask_sequence_file = $output_basename + '.masked'
-cp $mask_sequence_file $output_mask;
-
-## Write out standard file (default)
-## The default '.out' file from RepeatMasker has a 3-line header and spaces rather
-## than tabs. Remove the header and replace the whitespaces with tab
-#set $standard_file = $output_basename + '.out'
-tail -n +4 $standard_file | tr -s ' ' '\t' > $output_std;
-
-## Delete all temporary files
-rm $dirname -r;
-
-
-    </command>
-    <inputs>
-        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
-
-        <param name="nolow" type="boolean" label="No low complexity DNA" truevalue="-nolow" falsevalue="" checked="false" help="Does not mask low_complexity DNA or simple repeats."/>
-        <param name="noint" type="boolean" label="No interspersed repeats" truevalue="-noint" falsevalue="" checked="false" help="Only masks low complex/simple repeats (no interspersed repeats)."/>
-
-        <param name="norna" type="boolean" label="No small RNA genes" truevalue="-norna" falsevalue="" checked="false" help="Does not mask small RNA (pseudo) genes."/>
-
-        <!--
-            Specify the species or clade of the input sequence. The species name
-            must be a valid NCBI Taxonomy Database species name and be contained
-            in the RepeatMasker repeat database. The following collection is not complete.
-        -->
-        <param name="species" type="select" label="Species" help="The list is not complete, if you need other species contact your administrator.">
-            <option value="-species anopheles">anopheles</option>
-            <option value="-species arabidopsis">arabidopsis</option>
-            <option value="-species artiodactyl">artiodactyl</option>
-            <option value="-species aspergillus">aspergillus</option>
-            <option value="-species carnivore">carnivore</option>
-            <option value="-species cat">cat</option>
-            <option value="-species chicken">chicken</option>
-            <option value="-species 'ciona intestinalis'">ciona intestinalis</option>
-            <option value="-species 'ciona savignyi'">ciona savignyi</option>
-            <option value="-species cow">cow</option>
-            <option value="-species danio">danio</option>
-            <option value="-species diatoaea">diatoaea</option>
-            <option value="-species dog">dog</option>
-            <option value="-species drosophila">drosophila</option>
-            <option value="-species elegans">elegans</option>
-            <option value="-species fugu">fugu</option>
-            <option value="-species fungi" selected="true">fungi</option>
-            <option value="-species human">human</option>
-            <option value="-species maize">maize</option>
-            <option value="-species mammal">mammal</option>
-            <option value="-species mouse">mouse</option>
-            <option value="-species pig">pig</option>
-            <option value="-species rat">rat</option>
-            <option value="-species rice">rice</option>
-            <option value="-species rodentia">rodentia</option>
-            <option value="-species wheat">wheat</option>
-        </param>
-
-        <conditional name="adv_opts">
-            <param name="adv_opts_selector" type="select" label="Advanced Options">
-              <option value="basic" selected="True">Hide Advanced Options</option>
-              <option value="advanced">Show Advanced Options</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-
-
-              <param name="is_only" type="boolean" label="Mask only E coli insertion elements" truevalue="-is_only" falsevalue="" checked="false" help="Only clips E coli insertion elements out of fasta and .qual files."/>
-
-
-              <param name="slow_search" type="boolean" label="Slow search" truevalue="-s" falsevalue="" checked="false" help="0-5% more sensitive, 2-3 times slower than default."/>
-              <param name="quick_search" type="boolean" label="Quick search" truevalue="-q" falsevalue="" checked="false" help="5-10% less sensitive, 2-5 times faster than default."/>
-              <param name="rush_search" type="boolean" label="Rush search" truevalue="-qq" falsevalue="" checked="false" help="about 10% less sensitive, 4->10 times faster than default."/>
-
-              <param name="only_alus" type="boolean" label="Only Alus" truevalue="-alu" falsevalue="" checked="false" help="Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)."/>
-
-              <param name="gccalc" type="boolean" label="Use GC depended matrices, automaticly" truevalue="-gccalc" falsevalue="" checked="true" help="RepeatMasker calculates the GC content even for batch files/small seqs"/>
-
-              <param name="output_files" type="select" multiple="true" label="Additional output files">
-                  <option selected="true" value="summary">Summary file</option>
-                  <option value="gff">GFF file</option>
-                  <option value="html">HTML file</option>
-                  <option value="mask">Mask FastA file</option>
-              </param>
-
-
-              <param name="gc" type="integer" value="0" label="Use GC depended matrices" help="Use matrices calculated for 'number' percentage background GC level">
-                    <validator type="in_range" min="0" />
-                    <validator type="in_range" max="100" />
-              </param>
-
-            </when>
-        </conditional>
-
-    </inputs>
-    <outputs>
-        <data name="output_std" format="tabular" label="${tool.name} on ${on_string}: Standard" />
-        <data name="output_mask" format="fasta" label="${tool.name} on ${on_string}: Mask sequence">
-            <filter>
-                    (adv_opts['adv_opts_selector'] == 'advanced' and 'mask' in adv_opts['output_files'])
-            </filter>
-        </data>
-        <data name="output_summary" format="txt" label="${tool.name} on ${on_string}: Summary">
-            <filter>(
-                    (adv_opts['adv_opts_selector'] == 'advanced' and 'summary' in adv_opts['output_files'])
-                    or
-                    (adv_opts['adv_opts_selector'] == 'basic')
-                    )
-            </filter>
-        </data>
-        <data name="output_html" format="html" label="${tool.name} on ${on_string}: HTML">
-            <filter>(adv_opts['adv_opts_selector'] == 'advanced' and 'html' in adv_opts['output_files'])</filter>
-        </data>
-        <data name="output_gff" format="gff" label="${tool.name} on ${on_string}: GFF">
-            <filter>
-                    (adv_opts['adv_opts_selector'] == 'advanced' and 'gff' in adv_opts['output_files'])
-            </filter>
-        </data>
-    </outputs>
-    <requirements>
-        <requirement type="binary">RepeatMasker</requirement>
-    </requirements>
-    <help>
-    
-.. class:: warningmark
-
-
------
-
-**What it does**
-
-RepeatMasker is a program that screens DNA sequences for *interspersed repeats*
-and *low complexity* DNA sequences. The output of the program is a detailed
-annotation of the repeats that are present in the query sequence as well as a
-modified version of the query sequence in which all the annotated repeats have
-been masked (default: replaced by Ns).
-
------
-
-**How to read the results**
-
-
-
-The annotation file contains the cross_match output lines. It lists all best matches
-(above a set minimum score) between the query sequence and any of the sequences in
-the repeat database or with low complexity DNA. The term "best matches" reflects
-that a match is not shown if its domain is over 80% contained within the domain
-of a higher scoring match, where the "domain" of a match is the region in
-the query sequence that is defined by the alignment start and stop. These domains
-have been masked in the returned masked sequence file. In the output, matches are
-ordered by query name, and for each query by position of the start of the alignment.
-
-Example:
-
-======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
-SW score perc div. perc del. perc ins. query seq. q-pos begin q-pos end (left)    w complement matching repeat repeat class/family repeat-pos begin repeat-pos end (left)  ID
-======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
-    1306 15.6      6.2       0.0       HSU08988   6563        6781      \(22462)  C            MER7A           DNA/MER2_type       336              103            \(0)    1
-   12204 10.0      2.4       1.8       HSU08988   6782        7714      \(21529)  C            TIGGER1         DNA/MER2_type       2418             1493           \(0)    2
-     279  3.0      0.0       0.0       HSU08988   7719        7751      \(21492)  +            (TTTTA)n        Simple_repeat       1                33             \(0)    3
-    1765 13.4      6.5       1.8       HSU08988   7752        8022      \(21221)  C            AluSx           SINE/Alu            289              1              \(23)   4
-   12204 10.0      2.4       1.8       HSU08988   8023        8694      \(20549)  C            TIGGER1         DNA/MER2_type       1493             827            \(925)  5
-    1984 11.1      0.3       0.7       HSU08988   8695        9000      \(20243)  C            AluSg           SINE/Alu            305              1              \(5)    6
-   12204 10.0      2.4       1.8       HSU08988   9001        9695      \(19548)  C            TIGGER1         DNA/MER2_type       827              2              \(1591) 7
-     711 21.2      1.4       0.0       HSU08988   9696        9816      \(19427)  C            MER7A           DNA/MER2_type       122              2              \(224)  8
-======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= ==
-
-This is a sequence in which a Tigger1 DNA transposon has integrated into a MER7 DNA transposon copy.
-Subsequently two Alus integrated in the Tigger1 sequence. The simple repeat is derived from the
-poly A of the Alu element. The first line is interpreted like this:
-
-:Table description:
-
-1. **1306** = Smith-Waterman score of the match, usually complexity adjusted
-        The SW scores are not always directly comparable. Sometimes
-        the complexity adjustment has been turned off, and a variety of
-        scoring-matrices are used.
-
-#. **15.6** = % substitutions in matching region compared to the consensus
-#. **6.2** = % of bases opposite a gap in the query sequence (deleted bp)
-#. **0.0** = % of bases opposite a gap in the repeat consensus (inserted bp)
-#. **HSU08988** = name of query sequence
-#. **6563** = starting position of match in query sequence
-#. **7714** = ending position of match in query sequence
-#. **(22462)** = no. of bases in query sequence past the ending position of match
-#. **C**       = match is with the Complement of the consensus sequence in the database
-#. **MER7A**   = name of the matching interspersed repeat
-#. **DNA/MER2_type** = the class of the repeat, in this case a DNA transposon fossil of the MER2 group (see below for list and references)
-#. **2418**    = starting position of match in database sequence (using top-strand numbering)
-#. **1465**    = ending position of match in database sequence
-#. **(0)**     = no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match (so 0 means that the match extended all the way to the end of the repeat consensus sequence)
-#. **1**    = Identifier
-
-An asterisk (\*) in the final column (no example shown) indicates that there is
-a higher-scoring match whose domain partly (&lt;80%) includes the domain of this match. 
-
-Note that the SW score and divergence numbers for the three Tigger1 lines are identical.
-This is because the information is derived from a single alignment (the Alus were deleted
-from the query before the alignment with the Tigger element was performed).
-The program makes educated guesses about many fragments if they are derived from
-the same element (e.g. it knows that the MER7A fragments represent one insert).
-In a next version I can identify each element with a unique ID, if interest exists
-(this could help to represent repeats cleaner in graphic displays). 
-
-
--------
-
-**References**
-
-Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.
-
-http://www.repeatmasker.org/
-
-    </help>
-</tool>