diff snap_caller.xml @ 4:ffee8534a5c4

upgrade to mimodd version 0.1.6

--- a/snap_caller.xml	Wed Feb 11 09:26:43 2015 -0500
+++ b/snap_caller.xml	Thu Jun 04 17:52:04 2015 +0200
@@ -31,13 +31,17 @@
 		#if $str($set.filter_output) != "off":
 --filter-output $set.filter_output
 		#end if
-		#if $str($set.sort) != "off":
---sort $set.sort
+		#if $str($set.sort) == "off":
+--no-sort
+		#end if
+		#if $str($set.mmatch_notation) != "general":
+-X
 		#end if
-		#if $str($set.mmatch_notation) == "general":
--M
-		#end if
---max-mate-overlap '$set.max_mate_overlap'
+		#if $set.discard_overlapping_mates:
+--discard-overlapping-mates 
+	## remove ',' (and possibly adjacent whitespace) and replace with ' '
+	'#echo ("' '".join($set.discard_overlapping_mates.replace(" ", "").split(',')))#'
+        #end if
 --verbose
 "							
 	#end for
@@ -144,7 +148,7 @@
 	    <param name="filter_output" type="hidden" value="off"/>
 	    <param name="sort" type="hidden" value="0"/>
 	    <param name="mmatch_notation" type="hidden" value="general"/>
-	    <param name="max_mate_overlap" type="hidden" value="0" />
+	    <param name="discard_overlapping_mates" type="hidden" value="" />
       </when>
       
       ## change settings
@@ -154,10 +158,9 @@
     	<param name="slack" type="float" value="0.3" label="hash table slack size (default: 0.3)" help="Corresponds to the -h option of SNAP index."/>	
 
       ## paired-end specific options
-    	<param name="sp_min" type="integer" value="100" label="minimum spacing to allow between paired ends (default: 100)" help="Corresponds to the first value of the SNAP option -s."/>
-	    <param name="sp_max" type="integer" value="10000" label="maximum spacing to allow between paired ends (default: 10000)" help="Corresponds to the second value of the SNAP option -s."/>
-	    <param name="max_mate_overlap" type="float" value="0" label="Maximal overlap between the reads in a pair (as a fraction of their combined length; default: 0, no overlap allowed)" help="If the reads of a read pair overlap by more than this fraction of their combined length, they are filtered out" />
-
+    	<param name="sp_min" type="integer" value="100" label="minimum spacing to allow between paired ends (default: 100)" help="Corresponds to the first value of the SNAP option -s. Affects paired-end data only."/>
+	    <param name="sp_max" type="integer" value="10000" label="maximum spacing to allow between paired ends (default: 10000)" help="Corresponds to the second value of the SNAP option -s. Affects paired-end data only."/>
+	    <param name="discard_overlapping_mates" type="text" display="checkboxes" multiple="true" label="discard overlapping read pairs of type" help="Consider overlapping mate pairs of the given orientation type(s) anomalous and discard them; allowed values: RF, FR, FF, RR; multiple types may be specified as a comma-separated list and ALL can be used as a shortcut for discarding all overlapping mate pairs; leave blank to retain all overlapping pairs. Affects paired-end data only." />
     	<param name="maxdist" type="integer" value="8" label="edit distance (default: 8)" help="maximum edit distance allowed per read or pair (SNAP option -d); higher values allow more divergent alignments to be found, but increase the rate of misalignments."/>
 	    <param name="maxhits" type="integer" value="250" label="maximum hits per seed (default: 250)" help="Maximum hits to consider per seed (SNAP option -h); don't use a seed region in the alignment process if it matches more than maxhits regions in the reference genome. Higher values reduce the rate of misalignments, but reduce performance."/>
 	    <param name="confdiff" type="integer" value="2" label="confidence threshold (default: 2)" help="Confidence threshold (SNAP option -c); the minimum edit distance difference between two alternate alignments required to reject the poorer alignment as suboptimal; higher values increase the rate of ambiguously aligned reads."/>
@@ -225,11 +228,14 @@
 
    Optionally, a SAM header file can also be used to replace existing read-group information in a headered SAM/BAM input file. This can be used to resolve read-group ID conflicts between multiple input files at tool runtime.
 
-4) Currently, you cannot configure aligner-specific options separately for specific input files from within this Galaxy tool. If you need this advanced level of control, you should use the command line tool ``mimodd snap-batch``.
+5) The options available under *further parameter settings* can have **big** effects on the alignment quality. You are strongly encouraged to consult the `tool documentation`_ for detailed explanations of the available options.
+
+6) Currently, you cannot configure aligner-specific options separately for specific input files from within this Galaxy tool. If you need this advanced level of control, you should use the command line tool ``mimodd snap-batch``.
 
 .. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531
 .. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy
 .. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
+.. _tool documentation: http://mimodd.readthedocs.org/en/latest/tool_doc.html#snap
 
 </help>
 </tool>