From 871dfe4a6db9f0724855aef9ed149e047505eca4 Mon Sep 17 00:00:00 2001
From: Anton Nekrutenko <anton@bx.psu.edu>
Date: Fri, 24 Apr 2009 15:06:51 -0400
Subject: [PATCH] Added column info to MB wrapper

---
 static/welcome.html                     |  1 +
 tools/metag_tools/megablast_wrapper.xml | 35 ++++++++++++++++---------
 2 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/static/welcome.html b/static/welcome.html
index deb061514c8..7d0dc5049d7 100644
--- a/static/welcome.html
+++ b/static/welcome.html
@@ -14,6 +14,7 @@
       .current-quickie {
 	    width: 100%;
 	    background: black;
+	    borderRadius:10;
       }
       .quickie .head {
 	    font-size: 200%;
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 9ed440632b8..bbfa4226660 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -2,20 +2,20 @@
 	<description> compare short reads against nt and wgs databases</description>
 	<command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command>
 	<inputs>
-		<param name="source_select" type="select" display="radio" label="Choose target database">
+		<param name="input_query" type="data" format="fasta" label="Compare these sequences"/> 
+		<param name="source_select" type="select" display="radio" label="against target database">
 			<options from_file="blastdb.loc">
 			  <column name="name" index="0"/>
 			  <column name="value" index="0"/>
 			</options>
 		</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">
+		<param name="word_size" type="select" label="using word size" help="Size of best perfect match">
 			<option value="28">28</option>
 			<option value="16">16</option>
 		</param>
-		<param name="iden_cutoff" type="float" size="15" value="90.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" />
-        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Expectation value (-e)" />
-		<param name="filter_query" type="select" label="Filter query sequence (-F)">
+		<param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" />
+        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
+		<param name="filter_query" type="select" label="Filter out low complexity regions?">
             <option value="T">Yes</option>
             <option value="F">No</option>
 		</param>
@@ -49,18 +49,27 @@
 
 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.
 
-
 -----
 
-**Parameters**
+**Output format**
 
-- *Word size* (**-W**) : the minimal length of an exact match  
-- *Identity percentage cut-off* (**-p**) : the minimal identity for an alignment
-- *Expectation value* (**-e**) : the maximal expectation value for an alignment
-- *Filter query sequence* (**-F**) : mask low-complexity regions in the query sequence
+Output of this tool contains 13 columns delimited by Tabs:
 
+1. Id of your sequence 
+2. GI of the database hit 
+3. Length of the database hit
+4. % identity
+5. Alignment length
+6. # mismatches
+7. # gaps
+8. Start position in your sequence
+9. End position in your sequence
+10. Start position in database hit
+11. End position in database hit
+12. E-value
+13. Bit score
 
------
+-------
 
 **Reference**