diff --git a/tools/filters/remove_beginning.xml b/tools/filters/remove_beginning.xml
index 84ddc8742e5..6718a9b05a3 100644
--- a/tools/filters/remove_beginning.xml
+++ b/tools/filters/remove_beginning.xml
@@ -2,7 +2,7 @@
   <description>of a file</description>
   <command interpreter="perl">remove_beginning.pl $input $num_lines $out_file1</command>
   <inputs>
-    <param name="num_lines" size="5" type="integer" value="5" label="Remove first" help="lines"/>
+    <param name="num_lines" size="5" type="integer" value="1" label="Remove first" help="lines"/>
     <param format="txt" name="input" type="data" label="from"/>
   </inputs>
   <outputs>
diff --git a/tools/filters/sorter.xml b/tools/filters/sorter.xml
index c67eb4472ea..e6403dbf3be 100644
--- a/tools/filters/sorter.xml
+++ b/tools/filters/sorter.xml
@@ -5,12 +5,12 @@
     <param format="tabular" name="input" type="data" label="Sort Query" />
     <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" />
     <param name="order" type="select" label="in">
-      <option value="ASC">Ascending order</option>
       <option value="DESC">Descending order</option>
+      <option value="ASC">Ascending order</option>
     </param>
     <param name="style" type="select" label="Flavor">
-      <option value="alpha">Alphabetical sort</option>
       <option value="num">Numerical sort</option>
+      <option value="alpha">Alphabetical sort</option>
     </param>
   </inputs>
   <outputs>
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index cbbc558d1d6..ae32272707f 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -2,16 +2,15 @@
 	<description>for Metagenomics Projects</description>
 	<command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $disc_word $disc_type $filter_query ${GALAXY_DATA_INDEX_DIR}</command>
 	<inputs>
-		<param name="source_select" type="select" display="radio" label="Target database">
+		<param name="source_select" type="select" display="radio" label="Choose target database">
 			<options from_file="blastdb.loc" name_col="0" value_col="0"/>
 		</param>
 		<param name="input_query" type="data" format="fasta" label="Sequence file"/> 
 		<param name="word_size" type="select" label="Word size (-W)" help="Size of best perfect match">
 			<option value="28">28</option>
 			<option value="16">16</option>
-			<option value="12">12</option>
 		</param>
-		<param name="iden_cutoff" type="float" size="15" value="0.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" />
+		<param name="iden_cutoff" type="float" size="15" value="90.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" />
 		<param name="disc_word" type="integer" size="15" value="0" label="Length of a discontiguous word template (-t)" help="contiguous word if 0. Only support 16, 18, or 21."/>
 		<param name="disc_type" type="select" label="Type of a discontiguous word template (-N)">
 			<option value="0">0 - coding</option>
@@ -43,16 +42,15 @@
 	</tests>
 	<help>
 	
-.. class:: infomark
+.. class:: warningmark
 
-**TIP**. Searching might require few hours before returning the result.
+**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.  
 
 -----
 
 **What it does**
 
-This tool runs **megablast** (for information about megablast, please see the reference below) and search against a nucleotide database. 
-The query sequence could be any nucleotide sequences in fasta format.  
+This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues.
 
 
 -----
@@ -81,7 +79,7 @@ The query sequence could be any nucleotide sequences in fasta format.
 
 **Reference**
 
- **Megablast**: Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
+Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
 
 	</help>
 </tool>
diff --git a/tools/metag_tools/megablast_xml_parser.xml b/tools/metag_tools/megablast_xml_parser.xml
index bf2638c96db..b860df0d215 100644
--- a/tools/metag_tools/megablast_xml_parser.xml
+++ b/tools/metag_tools/megablast_xml_parser.xml
@@ -1,5 +1,5 @@
-<tool id="megablast_xml_parser" name="Parse megablast xml output">
-<description> </description>
+<tool id="megablast_xml_parser" name="Parse">
+<description>XML output from blast programs</description>
 <command interpreter="python">megablast_xml_parser.py $input1 $output1</command>
 <inputs>
 	<param name="input1" type="data" format="txt" label="Megablast XML output" />
@@ -20,40 +20,49 @@
 
 .. class:: warningmark 
 
-**IMPORTANT**. Please **zip** your xml file and upload the zipped file. This will help speeding up the process. (hint: under shell command, try: gzip -c your_xml_file > your_xml_file.gz)
-
-.. class:: infomark 
-
-**TIP**. To get xml output from megablast, add option **-m 7** in the command line.
+Blast XML output **must** be uploaded to Galaxy in zipped form.
  
 -----
 	
 **What it does**
 
-This tool is for users to upload their own megablast xml output and converts to tabular format, showing all information for retrieving alignment blocks.
+This tool will process XML output of any NCBI blast tool (if you run your own blast jobs, the XML output can be generated with **-m 7** option).
  
 -----
 
-**Example**
+**Output fields**
 
-- Query sequence::
- 	
- 	&gt;seq1
-	CGGACAGCGCCGCCACCAACAAAGCCACCA
- 
-- Parsed output::
- 
-   +------+------+-----------------+----------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-   |  Qid | Qlen |             Sid |     Slen |                                                                                         HSP                                                                                          |                                                                    
-   +------+------+-----------------+----------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-   | seq1 |   30 | gnl|BL_ORD_ID|0 |  5528445 | 59.96 | 8.38112e-11 | 1 | 30 | 5436010 | 5436039 | 1 | 1 | 30 | 30 | CGGACAGCGCCGCCACCAACAAAGCCACCA | CGGACAGCGCCGCCACCAACAAAGCCACCA |         ||||||||||||||||||||||||||||||        |
-   +------+------+-----------------+----------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+This tools returns tab-delimted output with the following fields::
 
------
+    Description                               Example
+    ----------------------------------------- ----------------- 
 
-**Reference**
+    1. Name of the query sequence             Seq1
+    2. Length of the query sequence           30
+    3. Name of target sequence                gnl|BL_ORD_ID|0
+    4. Length of target sequence              5528445
+    5. Alignment bit score                    59.96
+    6. E-value                                8.38112e-11
+    7. Start of alignment within query        1
+    8. End of alignment within query          30
+    9. Start of alignment within target       5436010
+   10. End of alignment within target         5436039
+   11. Query frame                            1
+   12. Target frame                           1
+   13. Number of identical bases within       29 
+       the alignment
+   14. Alignment length                       30 
+   15. Aligned portion (sequence) of query    CGGACAGCGCCGCCACCAACAAAGCCACCA
+   16. Aligned portion (sequence) of target   CGGACAGCGCCGCCACCAACAAAGCCATCA
+   17. Midline indicating positions of        ||||||||||||||||||||||||||| || 
+       matches within the alignment
+
+------
+       
+.. class:: infomark
+
+Note that this form of output does not contain alignment identify value. However, it can be computed by dividing the number of identical bases wityh the alignment (Field 13) by the alignment length (Field 14) using *Text Manipulation->Compute* tool 
 
- **Megablast**: Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
 
 
 </help>