# HG changeset patch
# User bgruening
# Date 1390041809 18000
# Node ID dc63d59e7bf82c072d2e488dc43094237fb4c4af
# Parent  468b59eae694612374e73e3377fa384440ce5db2
Uploaded

diff -r 468b59eae694 -r dc63d59e7bf8 segemehl.xml
--- a/segemehl.xml	Sat Jan 18 05:26:31 2014 -0500
+++ b/segemehl.xml	Sat Jan 18 05:43:29 2014 -0500
@@ -110,24 +110,27 @@
                     <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
                     <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
                 </repeat>
-                <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end) (default:5000)" />
+                <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" />
             </when>
         </conditional>
 
 
-        <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries (default:12)">
+        <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries" help="default: 12 (-m)">
             <validator type="in_range" min="1"/>
         </param>
-        <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment (default:85)" >
+        <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment" help="default: 85 (-A)" >
             <validator type="in_range" min="1" max="100"/>
         </param>
-        <param name="hitstrategy" type="integer" value="1" size="5" label="report only best scoring hits (=1) or all (=0) (default:1)" />
-        <param name="prime5" type="text" size="80" label="add 5' adapter (default:none)" />
-        <param name="prime3" type="text" size="80" label="add 3' adapter (default:none)" />
-        <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail"/>
-        <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter"/>
-        <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping"/>
-        <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position (might take a while!)"/>
+        <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)">
+            <option value="1">report only best scoring hits</option>
+            <option value="0">report all scoring hits</option>
+        </param>
+        <param name="prime5" type="text" size="80" label="add 5' adapter" help="default: none (-Q)" />
+        <param name="prime3" type="text" size="80" label="add 3' adapter" help="default: none (-P)"/>
+        <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/>
+        <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/>
+        <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="-C"/>
+        <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/>
     </inputs>
 
     <outputs>