# HG changeset patch
# User greg
# Date 1503318273 14400
# Node ID e994f439190cf85aa16d42859a6f644bb1953096
# Parent  01d22cb1bccc79c8d653048610be8f713c164ff8
Uploaded

diff -r 01d22cb1bccc -r e994f439190c meme_psp_gen.xml
--- a/meme_psp_gen.xml	Mon Aug 21 08:16:59 2017 -0400
+++ b/meme_psp_gen.xml	Mon Aug 21 08:24:33 2017 -0400
@@ -11,7 +11,11 @@
 -minw $adv.minw
 -maxw $adv.maxw
 $adv.alphabet
-#if $adv.report_scores_cond.report_scores:
+#if str($adv.triples_cond.triples) == 'yes':
+    -triples
+#end if
+#if str($adv.report_scores_cond.report_scores) == 'yes':
+    -reportscores
     2> '$output_tabular'
 #end if
 > '$output_psp'
@@ -28,7 +32,10 @@
                 <option value="-rna">RNA</option>
             </param>
             <conditional name="triples_cond">
-                <param name="triples" type="boolean" truevalue="-triples" falsevalue="" checked="False" label="Use spaced triples instead of whole-word matches?" help="Recommended for protein"/>
+                <param name="triples" type="select" label="Use spaced triples instead of whole-word matches?" help="Recommended for protein">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">yes</option>
+                </param>
                 <when value="no"/>
                 <when value="yes">
                     <param name="fixed_start" type="boolean" truevalue="-fixedstart" falsevalue="" checked="False" label="Allow triples to start anywhere within a site?" help="Select 'No' to only consider triples starting at the start of the site"/>
@@ -41,7 +48,10 @@
             <param name="max_range" type="boolean" truevalue="-maxrange" falsevalue="" checked="False" label="Choose the width with the biggest difference between minimum and maximum scores before scaling?" help="Select 'No' to choose the width with the biggest maximum score (before scaling)"/>
             <param name="raw" type="boolean" truevalue="-raw" falsevalue="" checked="False" label="Output scores instead of priors?"/>
             <conditional name="report_scores_cond">
-                <param name="report_scores" type="boolean" truevalue="-reportscores" falsevalue="" checked="False" label="Output primary and control file names, scores and widths?"/>
+                <param name="report_scores" type="select" label="Output primary and control file names, scores and widths?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">yes</option>
+                </param>
                 <when value="no"/>
                 <when value="yes">
                     <param name="verbose" type="boolean" truevalue="-verbose" falsevalue="" checked="False" label="Report frequency of each score?"/>