--- a/tophat_macros.xml	Thu May 07 15:16:15 2015 -0400
+++ b/tophat_macros.xml	Thu May 14 09:39:04 2015 -0400
@@ -23,14 +23,14 @@
       </param>
       <when value="No"/>
       <when value="Yes">
-        <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
-        <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
+        <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="--max-insertion-length; The maximum insertion length. The default is 3." />
+        <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="--max-deletion-length; The maximum deletion length. The default is 3." />
       </when>
     </conditional>    
   </macro>
   <macro name="own_junctionsConditional">
     <conditional name="own_junctions">
-      <param name="use_junctions" type="select" label="Use Own Junctions">
+      <param name="use_junctions" type="select" label="Do you want to supply your own junction data" help="The options below allow you validate your own list of known transcripts or junctions with your RNA-Seq data. Note that the chromosome names in the files provided with the options below must match the names in the Bowtie index.">
         <option value="No">No</option>
         <option value="Yes">Yes</option>
       </param>
@@ -42,7 +42,7 @@
           </param>
           <when value="No" />
           <when value="Yes">
-            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
+            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="-G/--GTF; TopHat with a set of gene model annotations and/or known transcripts, as a GTF 2.2 or GFF3 formatted file. If this option is provided, TopHat will first extract the transcript sequences and use Bowtie to align reads to this virtual transcriptome first. Only the reads that do not fully map to the transcriptome will then be mapped on the genome. The reads that did map on the transcriptome will be converted to genomic mappings (spliced as needed) and merged with the novel mappings and junctions in the final tophat output. Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat."/>
           </when>
         </conditional>
         <expand macro="raw_juncsConditional" />
@@ -59,12 +59,12 @@
       </param>
       <when value="No" />
       <when value="Yes">
-        <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
+        <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="-j/--raw-juncs; Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
       </when>
     </conditional>
   </macro>
   <macro name="no_novel_juncsParam">
-    <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
+    <param name="no_novel_juncs" type="select" label="Only look for supplied junctions" help="--no-novel-juncs; Only look for reads across junctions indicated in the supplied GFF or junctions file.">
       <option value="No">No</option>
       <option value="Yes">Yes</option>
     </param>