diff vvv2_display.xml @ 3:4bcde73a02de draft

Uploaded wrapper for 0.2.3.1 version

--- a/vvv2_display.xml	Fri Apr 12 07:48:10 2024 +0000
+++ b/vvv2_display.xml	Mon Jan 06 14:08:48 2025 +0000
@@ -1,27 +1,23 @@
-<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.2.1" python_template_version="3.9">
+<tool id="vvv2_display" name="vvv2_display: Display SNP proportions and CDS of an assembly in png image" version="0.2.3.1" python_template_version="3.9">
     <requirements>
-      <requirement type="package" version="0.2.1">vvv2_display</requirement>	      
+      <requirement type="package" version="0.2.3.1">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 '$snp_img' -o '$cov_depth' -e '$cov_depth_corr' -t '$snp_loc' -u '$snp_loc_summary' -j '$json_annot' -k '$bed_annot' -l '$correct_vcf' -m '$contig_limits'
+       vvv2_display.py -f '$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 '$contig_limits' '$cov_depth_scale'
     ]]></command>
     <inputs>
         <param type="data" name="vadr_fail_annotation" format="tabular" />
         <param type="data" name="vadr_pass_annotation" format="tabular" />
-        <param type="data" name="seqstat" format="txt" />
+        <param type="data" name="vadr_seqstat" format="txt" />
         <param type="data" name="vardict_vcf" format="vcf" />
+        <param type="integer" name="var_significant_thres" value="7" min="0" max="100" label="min int threshold to keep significant variant (%age)" format="int" />
+        <param type="select" name="cov_depth_scale" label="tells if cov depth scale (ordinate) is displayed with log10 (default) or linear scale" help="tells if cov depth scale (ordinate) is displayed with log10 (default) or linear scale">
+          <option value="">log10 scale</option>
+			    <option value="-y">linear scale</option>
+        </param>
         <param type="data" name="cov_depth" format="txt" />
     </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_loc_summary" format="txt" />
 	<!-- intermediate output files added for Galaxy compatibility -->
@@ -35,10 +31,12 @@
     </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_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="var_significant_thres" value="7"/>
+            <param name="cov_depth_scale" value="test_vvv2_display/res_covdepth.txt" />
             <output name="snp_img" file="test_vvv2_display/res_snp.png"/>	    
             <output name="snp_loc_summary" file="test_vvv2_display/res_snp_summary.txt"/>
 	          <!-- intermediate output files -->
@@ -47,8 +45,9 @@
             <output name="bed_annot" file="test_vvv2_display/res_vadr.4vardict.bed"/>
             <output name="correct_vcf" file="test_vvv2_display/res_correct.vcf"/>
             <output name="contig_limits" file="test_vvv2_display/contig_limits.txt"/>
+            <output name="cov_depth_corr" file="test_vvv2_display/res_covdepth_corrected.txt"/>
 	    <!-- end intermediate output files -->	    
-        </test>
+      </test>
     </tests>
     <help><![CDATA[
 [vvv2_display.py]