# HG changeset patch
# User wolma
# Date 1418160284 18000
# Node ID 840362af3e74c4b9c2f21c1ebc3c26e64bf0fdb9
# Parent  995e258cc46c9b0092578ae40ba5072a67906916
version 0_1_5

diff -r 995e258cc46c -r 840362af3e74 annotate_variants.xml
--- a/annotate_variants.xml	Wed Aug 13 07:11:40 2014 -0400
+++ b/annotate_variants.xml	Tue Dec 09 16:24:44 2014 -0500
@@ -1,17 +1,18 @@
 <tool id="annotate_variants" name="Variant Annotation">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
   <requirements>
-    <requirement type="package" version="0.1.3">mimodd</requirement>
+    <requirement type="package" version="0.1.5">mimodd</requirement>
   </requirements>
+  <version_command>mimodd version -q</version_command>
   <command>
   	mimodd annotate
 	
 	$inputfile
 	
 	#if $str($annotool.name)=='snpeff':
-	--genome ${annotool.genomeVersion}
+	--genome "${annotool.genomeVersion}"
 	    #if $annotool.ori_output:
-	--snpeff_out $snpeff_file
+	--snpeff-out $snpeff_file
 	    #end if
 	    #if $annotool.stats:
 	--stats $summary_file
@@ -37,7 +38,7 @@
 	--link ${formatting.formatter_file}
 	  #end if
 	  #if $formatting.species
-	--species ${formatting.species}
+	--species "${formatting.species}"
 	  #end if
 	#end if
 	
@@ -101,11 +102,11 @@
               <param name="chr" type="boolean" truevalue="-chr" falsevalue="" checked="false" label="prepend 'chr' to chromosome names, e.g., 'chr7' instead of '7'" />
               <param name="min_cov" type="integer" optional="true" label="minimum coverage (default = not used)" help="do not include variants with a coverage lower than this value"/>
               <param name="min_qual" type="integer" optional="true" label="minimum quality (default = not used)" help="do not include variants with a quality lower than this value"/>
-              <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no_downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/>
-              <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no_upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/>
-              <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no_intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/>
-              <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no_intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/>    
-              <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no_utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/>
+              <param name="no_ds" type="boolean" label="do not show downstream changes" truevalue="--no-downstream" falsevalue="" checked="false" help="annotation of effects on the downstream region of genes can be suppressed"/>
+              <param name="no_us" type="boolean" label="do not show upstream changes" truevalue="--no-upstream" falsevalue="" checked="false" help="annotation of effects on the upstream region of genes can be suppressed"/>
+              <param name="no_intron" type="boolean" label="do not show intron changes" truevalue="--no-intron" falsevalue="" checked="false" help="annotation of effects on introns of genes can be suppressed"/>
+              <param name="no_intergenic" type="boolean" label="do not show intergenic changes" truevalue="--no-intergenic" falsevalue="" checked="false" help="annotation of effects on intergenic regions can be suppressed"/>    
+              <param name="no_utr" type="boolean" label="do not show UTR changes" truevalue="--no-utr" falsevalue="" checked="false" help="annotation of effects on the untranslated regions of genes can be suppressed"/>
               <param name="ud" type="integer" optional="true" label="upstream downstream interval length (default = 5000 bases)" help="specify the upstream/downstream interval length, i.e., variants more than INTERVAL nts from the next annotated gene are considered to be intergenic"/>
             </when>
 	  </conditional>
@@ -140,7 +141,7 @@
 This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation.
 
 As output file formats HTML or plain text are supported.
-In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers.
+In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers and databases.
 
 The behavior of this feature depends on:
 
@@ -159,6 +160,10 @@
    If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species.
    If not, no hyperlinks will be generated and the html output will look essentially like plain text.
    
+   **TIP:**
+   MiModD's internal hyperlink formatting lookup tables are maintained and growing with every new version, but since weblinks are changing frequently as well, it is possible that you will encounter broken hyperlinks for your species of interest. In such a case, you can resort to two things: `tell us about the problem`_ to make sure it gets fixed in the next release and, in the meantime, use a custom file with hyperlink formatting instructions to overwrite the default entry for your species.
+   
+.. _tell us about the problem: mailto:mimodd@googlegroups.com
   </help>
 </tool>