Mercurial > repos > rnateam > locarna_pairwise

diff macros.xml @ 2:433601e9f132 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
author rnateam
date Sat, 21 Jan 2017 17:38:54 -0500
parents b06dc2bb3716
children f3f08a777c10
line wrap: on
line diff
--- a/macros.xml	Fri Jan 13 16:49:33 2017 -0500
+++ b/macros.xml	Sat Jan 21 17:38:54 2017 -0500
@@ -141,6 +141,12 @@
         #end if
     </token>
 
+    <token name="@HEURISTIC_SPARSE_ARGS@">
+           --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
+           --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold
+
+    </token>
+
     <token name="@CONSTRAINT_ARGS@">
         ## -------------------- constraint parameters
         $Constraints.lonely_pairs
@@ -232,6 +238,16 @@
                        'sequence length' (default: 0.0 = no effect)" />
     </xml>
     
+    <xml name="common_heuristic_parameters_sparse">
+        <param  name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
+                min="0.0" max="0.2"
+                label="Probability threshold for unpaired bases in loops" /> 
+
+        <param  name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 
+                min="0.0" max="0.2"
+                label="Probability threshold for base pairs in loops" />       
+    </xml>
+    
     <xml name="in_loop_ratio_parameters">
         <param  name="max_uil_length_ratio" argument="max-uil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
@@ -308,8 +324,7 @@
 
     <xml name="citations">
         <citations>
-            <citation
-            type="doi">10.1371/journal.pcbi.0030065</citation>
+            <citation type="doi">10.1371/journal.pcbi.0030065</citation>
             <citation type="doi">10.1261/rna.029041.111</citation>
             <citation type="doi">10.1093/bioinformatics/btv185</citation>
             <citation type="doi">10.1186/s12859-014-0404-0</citation>