diff vvv2_display.xml @ 20:882318c1e5b7 draft default tip

Uploaded, try correct vcf output def with conditional input

--- a/vvv2_display.xml	Thu Feb 05 14:15:52 2026 +0000
+++ b/vvv2_display.xml	Fri Feb 06 08:19:34 2026 +0000
@@ -3,7 +3,11 @@
       <requirement type="package" version="0.2.5.0">vvv2_display</requirement>	      
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-       vvv2_display.py -f '$vadr_fail_annotation' -p '$vadr_pass_annotation' -s '$vadr_seqstat' -n '$vardict_vcf' -r '$snp_img' -w '$var_significant_thres' -o '$cov_depth' -e '$cov_depth_corr' -t '$snp_loc' -u '$snp_loc_summary' -j '$json_annot' -k '$bed_annot' -l '$correct_vcf' -m '$contig_limits' -N '$contig_names' $cov_depth_scale $b_snp_vcf_summary
+       vvv2_display.py -f '$vadr_fail_annotation' -p '$vadr_pass_annotation' -s '$vadr_seqstat' -n '$vardict_vcf' -r '$snp_img' -w '$var_significant_thres' -o '$cov_depth' -e '$cov_depth_corr' -t '$snp_loc' -u '$snp_loc_summary' -j '$json_annot' -k '$bed_annot' -l '$correct_vcf' -m '$contig_limits' -N '$contig_names' $cov_depth_scale 
+       ## vcf significant output file option
+       #if str($option_snp_vcf_summary.boolean) == '2':
+           -x '${option_snp_vcf_summary.snp_vcf_summary_f}'
+       #end if
     ]]></command>
     <inputs>
         <param type="data" name="vadr_fail_annotation" format="tabular" />
@@ -16,17 +20,24 @@
 			    <option value="-y">linear scale</option>
         </param>
         <param type="data" name="cov_depth" format="txt" />
-        <param type="select" name="b_snp_vcf_summary" label="tells if vcf summary output file is created" help="tells if vcf summary output file is created">
-          <option value="">no summary vcf output</option>
-			    <option value="-x '$snp_vcf_summary' ">additional vcf summary output</option>
-        </param>
+        <conditional name="option_snp_vcf_summary">
+          <param type="select" name="boolean" label="tells if vcf summary output file is created" help="tells if vcf summary output file is created">
+            <option value="1">no summary vcf output</option>
+		  	    <option value="2">additional vcf summary output</option>
+          </param>
+          <when value="2">
+            <param type="data" name="snp_vcf_summary" format="vcf" argument="-x" help="provide the vcf summary output file name"/>
+                <expand macro="snp_vcf_summary_f"/>
+            </param>
+          </when>
+        </conditional>  
     </inputs>
     <outputs>
         <data name="snp_img" format="png" label="png image showing variants"/>
         <data name="snp_loc_summary" format="tabular" label="tsv file of significant variants only"/>
         <!-- present only if ask for summary vcf output-->
-        <data name="snp_vcf_summary" format="vcf" label="vcf file of significant variants only" optional="true">
-          <filter>b_snp_vcf_summary != "no summary vcf output"</filter>
+        <data name="option_snp_vcf_summary|snp_vcf_summary" format="vcf" label="vcf file of significant variants only" optional="true">
+          <filter>option_snp_vcf_summary['boolean'] == "1"</filter>
         </data>
 	<!-- intermediate output files added for Galaxy compatibility -->
         <data name="snp_loc" format="txt" hidden="true" label="tsv file of all variants"/>
@@ -40,16 +51,17 @@
     </outputs>
     <tests>
       <test>
-            <param name="vadr_fail_annotation" value="test_vvv2_display/res_vadr_fail.tbl"/>	
-            <param name="vadr_pass_annotation" value="test_vvv2_display/res_vadr_pass.tbl"/>
-            <param name="vadr_seqstat" value="test_vvv2_display/res_vadr.seqstat"/>
-            <param name="vardict_vcf" value="test_vvv2_display/res_vardict.vcf"/>
+            <param name="vadr_fail_annotation" value="test_vvv2_display/res_vadr_fail.tbl" ftype="tabular"/>	
+            <param name="vadr_pass_annotation" value="test_vvv2_display/res_vadr_pass.tbl" ftype="tabular"/>
+            <param name="vadr_seqstat" value="test_vvv2_display/res_vadr.seqstat" ftype="txt"/>
+            <param name="vardict_vcf" value="test_vvv2_display/res_vardict.vcf" ftype="vcf"/>
             <param name="var_significant_thres" value="7"/>
             <param name="cov_depth_scale" value="-y" />
             <param name="cov_depth" value="test_vvv2_display/res_covdepth.txt" />
+            <param name="option_snp_vcf_summary|boolean" value="2">
             <output name="snp_img" file="test_vvv2_display/res_snp.png" ftype="png"/>	    
             <output name="snp_loc_summary" file="test_vvv2_display/res_snp_summary.tsv" ftype="tabular"/>
-            <output name="snp_vcf_summary" file="test_vvv2_display/res_snp_summary.vcf" ftype="vcf"/>
+            <output name="option_snp_vcf_summary|snp_vcf_summary" file="test_vvv2_display/res_snp_summary.vcf" ftype="vcf"/>
 	          <!-- intermediate output files -->
             <output name="snp_loc" file="test_vvv2_display/res_snp.txt" ftype="txt"/>
 	          <output name="json_annot" file="test_vvv2_display/res_vadr.json" ftype="json"/>