small help and parameter name tweaks

tools/samtools/sam_pileup.xml

@@ -56,13 +56,13 @@
     </param>
     <param name="mapCap" type="integer" value="60" label="Where to cap mapping quality" />
     <conditional name="c">
-      <param name="consensus" type="select" label="Whether or not to call the consensus sequence using the MAQ consensus model">
-        <option value="no">Don't use MAQ consensus model</option>
-        <option value="yes">Use the MAQ consensus model</option>
+      <param name="consensus" type="select" label="Call consensus according to MAQ model?">
+        <option selected="true" value="no">No</option>
+        <option value="yes">Yes</option>
       </param> 
       <when value="no" />
       <when value="yes">
-        <param name="theta" type="float" value="0.85" label="Theta paramter (error dependency coefficient) in the MAQ consensus calling model" />
+        <param name="theta" type="float" value="0.85" label="Theta parameter (error dependency coefficient) in the MAQ consensus calling model" />
         <param name="hapNum" type="integer" value="2" label="Number of haplotypes in the sample" help="Greater than or equal to 2" />
         <param name="fraction" type="float" value="0.001" label="Expected fraction of differences between a pair of haplotypes" />
         <param name="phredProb" type="integer" value="40" label="Phred probability of an indel in sequencing/prep" />
@@ -77,10 +77,69 @@
     	
 **What it does**   	
 
-Uses SAMTools_' pileup command to produce a file in the pileup format based on the provided BAM file. 
+Uses SAMTools_' pileup command to produce a pileup dataset from a provided BAM dataset. It generated two types of pileup datasets depending on chosen options. If *Call consensus according to MAQ model?* option is set to **No**, the tool produces simple pileup. If the option is set to **Yes**, a ten column pileup dataset with consensus is generated. Both types of datasets are briefly summarized below.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
 
+------
+
+**Types of pileup datasets**
+
+The description of pileup format below is largely based on information that can be found on SAMTools_ documentation page. The 6- and 10-column variants are described below.
+
+.. _SAMTools: http://samtools.sourceforge.net/pileup.shtml
+
+**Six column pileup**::
+
+    1    2  3  4        5        6
+ ---------------------------------   
+ chrM  412  A  2       .,       II
+ chrM  413  G  4     ..t,     IIIH
+ chrM  414  C  4     ...a     III2
+ chrM  415  C  4     TTTt     III7
+   
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Coverage (# reads aligning over that position)
+       5 Bases within reads where (see Galaxy wiki for more info)
+       6 Quality values (phred33 scale, see Galaxy wiki for more)
+       
+**Ten column pileup**
+
+The `ten-column`__ pileup incoroporates additional consensus information generated with *-c* option of *samtools pileup* command::
+
+
+    1    2  3  4   5   6   7   8       9       10
+ ------------------------------------------------
+ chrM  412  A  A  75   0  25  2       .,       II
+ chrM  413  G  G  72   0  25  4     ..t,     IIIH
+ chrM  414  C  C  75   0  25  4     ...a     III2
+ chrM  415  C  T  75  75  25  4     TTTt     III7
+
+where::
+
+  Column Definition
+ ------- ----------------------------
+       1 Chromosome
+       2 Position (1-based)
+       3 Reference base at that position
+       4 Consensus bases
+       5 Consensus quality
+       6 SNP quality
+       7 Maximum mapping quality
+       8 Coverage (# reads aligning over that position)
+       9 Bases within reads where (see Galaxy wiki for more info)
+      10 Quality values (phred33 scale, see Galaxy wiki for more)
+
+
+.. __: http://samtools.sourceforge.net/cns0.shtml
+
+
   </help>
 </tool>
 

tools/samtools/sam_to_bam.xml

@@ -51,7 +51,7 @@
 
 **What it does**
 
-This tool uses the SAMTools_ toolkit to produce a BAM file based on a sorted input SAM file.
+This tool uses the SAMTools_ toolkit to produce a indexed BAM file based on a sorted input SAM file.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml