diff roary.xml @ 3:15ca041134a9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary commit 9c9db9f5e815e6a9b55c4adf378c7aa6a76a58da"

--- a/roary.xml	Fri Oct 20 04:30:53 2017 -0400
+++ b/roary.xml	Wed Aug 21 11:11:15 2019 -0400
@@ -1,18 +1,18 @@
-<tool id="roary" name="Roary" version="3.10.2">
+<tool id="roary" name="Roary" version="3.12.0+galaxy0">
     <description>the pangenome pipeline - Quickly generate a core gene alignment from gff3 files</description>
     
     <requirements>
-      <requirement type="package" version="3.10.2">roary</requirement>
+      <requirement type="package" version="3.12.0">roary</requirement>
     </requirements>
     
     <command detect_errors="exit_code"><![CDATA[
         
-        #for $counter, $gff in enumerate($gff_input.gffs)
-          cp $gff temp${counter}.gff &&
+        #for $gff in $gff_input.gffs
+          cp $gff '${gff.element_identifier}'.gff &&
         #end for
-                
+
         roary
-          -f out 
+          -f out
           -p \${GALAXY_SLOTS:-1}
           -e
           -n
@@ -22,8 +22,8 @@
           $advanced.split_para
           -t '$advanced.trans_tab'
           -iv '$advanced.mcl'
-          
-          temp*.gff
+
+          *.gff
           
     ]]></command>
     
@@ -34,10 +34,10 @@
           <option value="collection">Collection</option>
         </param>
         <when value="individual">
-          <param name="gffs" type="data" multiple="true" format="gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
+          <param name="gffs" type="data" multiple="true" format="gff,gff3" label="select gff inputs to Roary" help="Select the files you wish to send to Roary, must be in gff3 format with the sequence data at the end of the file." />
         </when>
         <when value='collection'>
-          <param name="gffs" type="data_collection" collection_type="list" format="gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
+          <param name="gffs" type="data_collection" collection_type="list" format="gff,gff3" label="Dataset collection to submit to Roary" help="A dataset list collection of gff3 files to send to Roary for analysis." />
         </when>
       </conditional>
       <param name="percent_ident" type="integer" label="minimum percentage identity for blastp" help="Sets the minimum percentage identity for protein matches" value="95"/>
@@ -171,7 +171,7 @@
     ]]></help>
     
     <citations>
-        <citation type="doi">http://doi.org/10.1093/bioinformatics/btv421</citation>
+        <citation type="doi">10.1093/bioinformatics/btv421</citation>
     </citations>
     
-</tool>
\ No newline at end of file
+</tool>