add all possible outputs, update version to 0.1.8

ANSES-Ploufragan · Mar 1, 2023 · 2b2c91f · 2b2c91f
1 parent 06e04d7
commit 2b2c91f
Showing 1 changed file with 25 additions and 6 deletions.
diff --git a/src/vvv2_display.xml b/src/vvv2_display.xml
@@ -1,13 +1,13 @@
-<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.1.7" python_template_version="3.9">
+<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.1.8" python_template_version="3.9">
     <requirements><!--
         only for tools used before, not for vvv2_display itself
         <requirement type="package" version="1.4.1">vadr</requirement>
         <requirement type="package" version="1.8.3">vardict-java</requirement>
       <requirement type="package" version="3.5.0">r-base</requirement> -->
-      <requirement type="package" version="0.1.7">vvv2_display</requirement>	      
+      <requirement type="package" version="0.1.8">vvv2_display</requirement>	      
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-       vvv2_display.py -f '$vadr_fail_annotation' -p '$vadr_pass_annotation' -s '$seqstat' -n '$vardict_vcf' -r '$snp_img'
+       vvv2_display.py -f '$vadr_fail_annotation' -p '$vadr_pass_annotation' -s '$seqstat' -n '$vardict_vcf' -r '$snp_img' -t '$snp_loc' -j '$json_annot' -k '$bed_annot' -l '$correct_vcf'
     ]]></command>
     <inputs>
         <param type="data" name="vadr_fail_annotation" format="tabular" />
@@ -16,17 +16,36 @@
         <param type="data" name="vardict_vcf" format="vcf" />
     </inputs>
     <outputs>
+	<!-- <data name="json_annot" format="txt">
+           <discover_datasets pattern="(?P&lt;designation&gt;.+)\.json" format="json" directory="." visible="true" />
+	 </data>
+	 <data name="bed_annot" format="txt">
+           <discover_datasets pattern="(?P&lt;designation&gt;.+)_vardict\.bed" format="bed" directory="." visible="true" />
+	 </data>
+	 <data name="corrected_vcf" format="txt">
+           <discover_datasets pattern="(?P&lt;designation&gt;.+)_correct\.vcf" format="vcf" directory="." visible="true" />
+	 </data> -->
         <data name="snp_img" format="png" />
-        <data name="snp_descr" format="txt" from_work_dir="test_vvv2_display/res.snp.txt" />
+        <data name="snp_loc" format="txt" />
+	<!-- intermediate output files added for Galaxy compatibility -->	
+        <data name="json_annot" format="json" />
+        <data name="bed_annot" format="bed" />
+        <data name="correct_vcf" format="vcf" />
+	<!-- end intermediate output files added for Galaxy compatibility -->		
     </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"/>
-            <output name="snp_img" file="test_vvv2_display/res_snp.png"/>
-            <output name="snp_descr" file="test_vvv2_display/res_snp.txt"/>
+            <output name="snp_img" file="test_vvv2_display/res_snp.png"/>	    
+            <output name="snp_loc" file="test_vvv2_display/res_snp.txt"/>
+	    <!-- intermediate output files -->
+	    <output name="json_annot" file="test_vvv2_display/res_vadr.json"/>
+            <output name="bed_annot" file="test_vvv2_display/res_vadr.4vardict.bed"/>
+            <output name="correct_vcf" file="test_vvv2_display/res_correct.vcf"/>
+	    <!-- end intermediate output files -->	    
         </test>
     </tests>
     <help><![CDATA[