--- a/freebayes.xml	Mon Mar 10 11:15:27 2025 +0000
+++ b/freebayes.xml	Wed May 07 05:35:03 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
     <description>bayesian genetic variant detector</description>
     <xrefs>
         <xref type="bio.tools">freebayes</xref>
@@ -39,10 +39,10 @@
         #end if
     #end for
 
-    ## Tabixize optional input_variant_vcf file (for --variant-input option)
+    ## For --variant-input option, create symlinks to vcf.bgzip input and its accompanying tabix index
     #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
         ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
-        ln -s -f '${Tabixized_input}' input_variant_vcf.vcf.gz.tbi &&
+        ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
     #end if
 
     ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
@@ -129,7 +129,7 @@
                     --cnv-map '${options_type.optional_inputs.A}'
                 #end if
                 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-                    --variant-input 'input_variant_vcf.vcf.gz'  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
+                    --variant-input 'input_variant_vcf.vcf.gz'
                     ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
                 #end if
                 #if $options_type.optional_inputs.haplotype_basis_alleles:
@@ -365,9 +365,7 @@
                             <when value="do_not_provide" />
                             <when value="provide_vcf">
                                 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
-                                       label="Use variants reported in this VCF dataset as input to the algorithm">
-                                    <conversion name="Tabixized_input" type="tabix" />
-                                </param>
+                                       label="Use variants reported in this VCF dataset as input to the algorithm"/>
                                 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
                                        label="Only provide variant calls and genotype likelihoods for sites in VCF" />
                             </when>
@@ -640,15 +638,25 @@
             <param name="min_coverage" value="14"/>
             <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
         </test>
+        <!-- Test that user-provided (variant-input option) sites are included in output -->
         <test>
             <param name="reference_source_selector" value="history" />
             <param name="processmode" value="individual" />
             <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
             <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
-            <param name="options_type_selector" value="naive_w_filters"/>
-            <param name="coverage_options_selector" value="set" />
-            <param name="min_coverage" value="14"/>
-            <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
+            <param name="options_type_selector" value="full"/>
+            <conditional name="optional_inputs">
+                <param name="optional_inputs_selector" value="set" />
+                <conditional name="input_variant_type">
+                    <param name="input_variant_type_selector" value="provide_vcf" />
+                    <param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
+                </conditional>
+            </conditional>
+            <output name="output_vcf">
+                <assert_contents>
+                    <has_line_matching expression="phiX174&#009;1134&#009;\.&#009;A&#009;\.&#009;.+"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="reference_source_selector" value="history" />