--- a/bacteria_tradis.xml	Mon Jul 04 07:29:27 2022 +0000
+++ b/bacteria_tradis.xml	Wed Mar 13 14:56:52 2024 +0000
@@ -3,6 +3,7 @@
     <macros>
           <import>macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
         <![CDATA[
@@ -25,6 +26,7 @@
                 #if str($tranposon_tag.use) == "yes":
                     -m '$tranposon_tag.nb_mismatches'
                     -t '$tranposon_tag.sequence'
+                    -td '$tranposon_tag.tagdir'
                 #end if
             2>&1 
         ]]>
@@ -43,13 +45,15 @@
             <when value="modify">
             
                 <conditional name="set_kmers_options">
-                    <param name="set" type="boolean" label="Modify kmers parameters" truevalue='yes' falsevalue='no' />
+                    <param name="set" type="select" label="Modify kmers parameters">
+                        <option value="yes">Yes</option>
+                        <option value="no">No</option>
+                    </param>
                     <when value="yes">
-                      <param name="kmer_length" type="integer" value="" min="9" max="20" label=" Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." />
-                     <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." /> 
-                     </when>
-                     <when value="no">
-                     </when>
+                        <param name="kmer_length" type="integer" value="" min="9" max="20" label="Length of kmers hashed (--smalt_k)" help=" The minimum length of an exact match between a read and the genome needed to trigger an alignment attempt. Appropriate values are between ~10 and 20 for bacterial genomes depending on read length. Lower values lead to increased sensitivity at the expense of runtime." />
+                        <param name="step_size" type="integer" value="" min="1" max="15" label="Step size for smalt kmers (--smalt_s)" help=" Distance between the start of hashed kmers. Appropriate values are between 1 and ~15, but should be less than --smalt_k to ensure kmers overlap. Lower values lead to increased sensitivity at the expense of runtime." /> 
+                    </when>
+                    <when value="no"/>
                 </conditional>
                 
                 <param name="min_percentage" type="float" value="0.96" min="0" max="1" label="Minimum percentage of identical bases between read and reference (--smalt_y)" help="May be lowered to improve sensitivity in the case of low quality or short reads." />         
@@ -62,20 +66,19 @@
         </conditional>
 
         <conditional name="tranposon_tag">
-            <param name="use" type="boolean" truevalue="yes" falsevalue="no" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping." />
-            
+            <param name="use" type="select" label="Search for a tranposon tag" help="Use with data containing a transposon tag attached to the reads. Only reads containing the transposon tag will be processed, and the tag will be removed before mapping.">
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
             <when value="yes">
-                
                 <param name="sequence" type="text" value="" help="" /> 
                 <param name="nb_mismatches" type="integer" value="2" min="0" help="If there is evidence for low-quality bases in the transposon tag (from FastQC, for instance), setting this to 1 or 2 may result in higher recovery of insertion sites. Higher than 2 is not advisable with the typical transposon tag lengths (10 - 12 bases) produced by TraDIS protocols, but may be appropriate with protocols that produce significantly longer transposon tags." />         
                 <param name="tagdir" type="select" label="Direction of the transposon tag" help="" >
                     <option value="3" selected="true">3'</option>
-                    <option value="5">5bacteria_tradis.xml'</option>
+                    <option value="5">5'</option>
                 </param>
-                 
             </when>
-            <when value="no">       
-            </when>
+            <when value="no"/>
         </conditional>