diff galaxy/tools/config_builder/config_builder.xml @ 7:4bfb3a8dd955 draft

Bug fixes

--- a/galaxy/tools/config_builder/config_builder.xml	Fri Mar 08 18:42:31 2019 -0500
+++ b/galaxy/tools/config_builder/config_builder.xml	Sun Mar 10 00:07:09 2019 -0500
@@ -113,7 +113,8 @@
                         variant evidence"/>
                     </when>
                 </conditional>
-                <param name="snp_fine" type="boolean" label="Consider SNP as a fine datatype"/>
+                <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp"
+                       label="Consider SNP as a fine datatype"/>
                 <param name="snp_threshold" type="integer" value="2500" min="0"
                        label="Correlation clustering threshold for MLST"/>
             </when>
@@ -164,7 +165,8 @@
                         kmer is seen to be considered present in the sample"/>
                     </when>
                 </conditional>
-                <param name="mlst_fine" type="boolean" label="Consider MLST as a fine datatype"/>
+                <param name="mlst_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst"
+                       label="Consider MLST as a fine datatype"/>
                 <param name="mlst_threshold" type="integer" value="300" min="0"
                        label="Correlation clustering threshold for MLST"/>
             </when>
@@ -173,7 +175,8 @@
         <conditional name="prince">
             <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
             <when value="true">
-                <param name="cnv_fine" type="boolean" label="Consider CNV as a fine datatype"/>
+                <param name="cnv_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv"
+                       label="Consider CNV as a fine datatype"/>
                 <param name="cnv_threshold" type="integer" value="100" min="0"
                        label="Correlation clustering threshold for CNV"/>
             </when>
@@ -192,7 +195,8 @@
                         of unique kmers in the input set"/>
                     </when>
                 </conditional>
-                <param name="kwip_fine" type="boolean" label="Consider kWIP as a fine datatype"/>
+                <param name="kwip_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip"
+                       label="Consider kWIP as a fine datatype"/>
                 <param name="kwip_threshold" type="float" value="0.4" min="0"
                        label="Correlation clustering threshold for kWIP"/>
             </when>
@@ -201,7 +205,8 @@
         <conditional name="spotyping">
             <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
             <when value="true">
-                <param name="spoligo_fine" type="boolean" label="Consider spoligotype as a fine datatype"/>
+                <param name="spoligo_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo"
+                       label="Consider spoligotype as a fine datatype"/>
                 <param name="spoligo_threshold" type="integer" value="8" min="0"
                        label="Correlation clustering threshold for Spoligotyping"/>
             </when>