diff abricate.xml @ 8:b734db305578 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit fc114fbebd3b866c33d2ad95b028cb719651689a"

--- a/abricate.xml	Tue Oct 29 19:24:59 2019 -0400
+++ b/abricate.xml	Wed Apr 22 18:44:06 2020 -0400
@@ -20,12 +20,15 @@
         #set $sample_name = re.sub('[^\w\-_\.]', '_', $file_input.element_identifier)
 
         ln -sf '${file_input}' ${sample_name} &&
-        
+
         abricate ${sample_name}
         $adv.no_header
         #if $adv.min_dna_id
             --minid=$adv.min_dna_id
         #end if
+        #if $adv.min_cov
+            --mincov=$adv.min_cov
+        #end if
         --db=$adv.db
         > '$report'
     ]]></command>
@@ -41,9 +44,12 @@
                 <option value="resfinder" selected="true">Resfinder</option>
                 <option value="plasmidfinder">PlasmidFinder</option>
                 <option value="vfdb">VFDB</option>
+                <option value="megares">megares</option>
+                <option value="ecoli_vf">Ecoli_VF</option>
             </param>
             <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
-            <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
+            <param name="min_dna_id" argument="--minid" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %identity" />
+            <param name="min_cov" argument="--mincov" type="float" value="80" min="0" max="100" optional="true" label="Minimum DNA %coverage" />
         </section>
     </inputs>
 
@@ -78,14 +84,28 @@
             <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test 4 - Min DNA ID 100 -->
+        <!-- Advanced test 4 - Changed DB to megares -->
+        <test>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="db" value="megares"/>
+            <output name="report" ftype="tabular" file="output_db-megares.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test 5 - Min DNA ID 100 -->
         <test>
             <param name="file_input" value="MRSA0252.fna"/>
             <param name="min_dna_id" value="100"/>
             <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
         </test>
 
-        <!-- Filetype test 5 - input a gbk -->
+        <!-- Advanced test 6 - Min Coverage 100 -->
+        <test>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="min_cov" value="100"/>
+            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
+        </test>
+
+        <!-- Filetype test 7 - input a gbk -->
         <test>
             <param name="file_input" value="test.gbk"/>
             <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>