Mercurial > repos > iuc > virannot_otu

diff virAnnot_otu.xml @ 2:96aafcc372f7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
author iuc
date Tue, 13 May 2025 11:51:51 +0000
parents 7e160902125e
children
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line diff
--- a/virAnnot_otu.xml	Sun Sep 08 14:08:48 2024 +0000
+++ b/virAnnot_otu.xml	Tue May 13 11:51:51 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="virannot_otu" name="virAnnot OTU" version="1.1.0+galaxy0" profile="21.05">
+<tool id="virannot_otu" name="virAnnot OTU" version="@TOOL_VERSION@+galaxy0" profile="21.05">
     <description>create viral OTUs based on RPS and Blast annotations</description>
     <macros>
         <import>macros.xml</import>
@@ -41,6 +41,7 @@
     -vp '$viral_portion'
     -mpl '$min_prot_length'
     -tp '$__tool_directory__/'
+    -m '$merge_rdrp'
     -o otu_output
 
     && zip -r out.zip otu_output
@@ -66,6 +67,10 @@
             <option value="150">150</option>
             <option value="200">200</option>
         </param>
+        <param type="select" name="merge_rdrp" label="Do you want to create a merge of RdRp domain ?">
+            <option value="yes">Yes</option>
+            <option value="no" selected="true">No</option>
+        </param>
     </inputs>
     <outputs>
         <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" />
@@ -74,7 +79,7 @@
     <tests>
         <test>
             <param name="blast_files" value="input_otu_blast_s1.tab,input_otu_blast_s2.tab"/>
-            <param name="rps_files" value="rps_s1_out.tab,rps_s2_out.tab"/>
+            <param name="rps_files" value="input_otu_rps_s1.tab,input_otu_rps_s2.tab"/>
             <param name="fasta_files" value="input_otu_s1.fasta,input_otu_s2.fasta"/>
             <param name="percentage" value="90"/>
             <param name="viral_portion" value="0.3"/>
@@ -87,6 +92,22 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="rps_files" value="input_otu_rps_s1.tab,input_otu_rps_s2.tab"/>
+            <param name="fasta_files" value="input_otu_s1.fasta,input_otu_s2.fasta"/>
+            <param name="percentage" value="90"/>
+            <param name="viral_portion" value="0.3"/>
+            <param name="min_prot_length" value="100"/>
+            <param name="merge_rdrp" value="yes"/>
+            <!-- check created zip -->
+            <output name="archive_output">
+                <assert_contents>
+                    <has_archive_member path=".*\/index.html" />
+                    <has_archive_member path=".*\/RdRp_merge" />
+                    <has_archive_member path=".*\/otu_stats.xlsx" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[