changeset 5:8d746b3723c6 draft

Uploaded

--- a/fastani_db/fastani.xml	Mon May 30 02:25:57 2022 +0000
+++ b/fastani_db/fastani.xml	Mon May 30 11:38:53 2022 +0000
@@ -20,19 +20,36 @@
 
     ### COMMAND ###
 
-    fastANI --ql query.lst --rl ref.lst -o output -t "\${GALAXY_SLOTS:-1}"
+    fastANI --ql query.lst --rl ref.lst -o output -t "\${GALAXY_SLOTS:-1}"; 
+
+    ### FILTER OUTPUT ###
+    #if $filter_select=="top"
+      cp output output.tmp && head -n 1 output.tmp > output;
+    #else if $filter_select=="per"
+      awk '{ if($3>$percut) {print $1,"\t",$2,"\t",$3,"\t",$4,"\t",$5;}}' output > output.tmp; mv output.tmp output; 
+    #end if 
 
     ]]></command>
     <inputs>
         <param name="query" type="data" format="fasta" multiple="true" label="Query Sequence(s)"
         help="Specify any number of query sequences in fasta format as input." />
-
-          <!-- DATABASE INPUT-->
+        <!-- DATABASE INPUT-->
         <param name="fastani_database" label="Select a database" type="select">
           <options from_data_table="fastani">
             <validator message="No database is available" type="no_options" />
           </options>
         </param>
+        <conditional name="filter"> 
+          <param name="filter_select" type="select" label="Filter Output">
+            <option value="top">Top Hit</option>
+            <option value="per">Percent Cutoff</option>
+          </param>
+          <when value="per">
+            <param name="percut" type="float" label="Percent Match between 70 and 100" value="70">
+              <validator type="in_range" message="Must be float(70,100)." min="70" max="100"/>
+            </param> 
+          </when>  
+	</conditional>
     </inputs>
     <outputs>
         <data name="output" format="tabular" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>