diff exonerate.xml @ 3:a03dead1bede draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate commit a141c63903d1a598569985e400125d4e7de42801"

--- a/exonerate.xml	Fri Jun 28 11:21:08 2019 -0400
+++ b/exonerate.xml	Sun Mar 01 04:48:34 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy1">
+<tool id="exonerate" name="Exonerate" profile="16.04" version="@VERSION@+galaxy2">
     <description>pairwise sequence comparison</description>
     <macros>
 	<import>macros.xml</import>
@@ -32,6 +32,16 @@
             --querytype dna --targettype dna
         #end if
 
+        #if $minintron
+            --minintron ${minintron}
+        #end if
+
+        #if $maxintron
+            --maxintron ${maxintron}
+        #end if
+
+        --cores \${GALAXY_SLOTS:-1}
+
         #if str($outformat) == "alignment"
             --showalignment yes --showvulgar no > '${output_ali}'
         #elif str($outformat) == "targetgff"
@@ -40,7 +50,10 @@
             --showalignment no --showvulgar no --showtargetgff no --showquerygff yes > '${output_gff}'
         #end if
 
-        --cores \${GALAXY_SLOTS:-1}
+        ## Produce a more standard GFF3
+        #if str($outformat) in ["targetgff", "querygff"]
+            && python '$__tool_directory__/exonerategff_to_gff3.py' '${output_gff}' > '${output_gff3}'
+        #end if
     ]]></command>
 
     <inputs>
@@ -83,9 +96,14 @@
         <param name='score' type='integer' min="0" max="10000" value="100" label="Score threshold for gapped alignment"/>
         <param name='percent' type='float' min="0" max="100" value="0.0" label="Report alignment over a percentage of the maximum score attainable by each query"/>
         <param name='bestn' type='integer' min="0" max="10000" value="0" label="Report best N results per query (0 to report all)"/>
+        <param argument='--minintron' type='integer' optional="true" label="Minimum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
+        <param argument='--maxintron' type='integer' optional="true" label="Maximum intron length limit" help="This is not a hard limit - it only affects size of introns which are sought during heuristic alignment."/>
     </inputs>
     <outputs>
-        <data name="output_gff" format="gff" label="${tool.name} on $on_string">
+        <data name="output_gff" format="gff" label="${tool.name} on $on_string - Raw GFF">
+            <filter>outformat != 'alignment'</filter>
+        </data>
+        <data name="output_gff3" format="gff3" label="${tool.name} on $on_string - GFF3">
             <filter>outformat != 'alignment'</filter>
         </data>
         <data name="output_ali" format="txt" label="${tool.name} on $on_string">
@@ -101,6 +119,7 @@
             </conditional>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="out_target.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -110,6 +129,7 @@
             </conditional>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="out_target.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_target.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -119,6 +139,7 @@
             </conditional>
             <param name="outformat" value="querygff"/>
             <output name="output_gff" file="out_query.gff" lines_diff="8"/>
+            <output name="output_gff3" file="out_query.gff3" lines_diff="8"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -138,6 +159,7 @@
             <param name="model" value="est2genome"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="est2genome.gff" lines_diff="4"/>
+            <output name="output_gff3" file="est2genome.gff3" lines_diff="4"/>
         </test>
         <test>
             <param name="query" value="proteome.fa"/>
@@ -148,6 +170,7 @@
             <param name="model" value="protein2genome"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="protein2genome.gff" lines_diff="2"/>
+            <output name="output_gff3" file="protein2genome.gff3" lines_diff="2"/>
         </test>
         <test>
             <param name="query" value="genome.fa"/>
@@ -158,6 +181,20 @@
             <param name="model" value="coding2coding"/>
             <param name="outformat" value="targetgff"/>
             <output name="output_gff" file="coding2coding.gff" lines_diff="4"/>
+            <output name="output_gff3" file="coding2coding.gff3" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="query" value="transcriptome.fa"/>
+            <conditional name="ref_seq">
+                <param name="ref_seq_selector" value="personal"/>
+                <param name="input_fasta" value="genome.fa"/>
+            </conditional>
+            <param name="model" value="est2genome"/>
+            <param name="outformat" value="targetgff"/>
+            <param name="minintron" value="100"/>
+            <param name="maxintron" value="200"/>
+            <output name="output_gff" file="est2genome_introns.gff" lines_diff="6"/>
+            <output name="output_gff3" file="est2genome_introns.gff3" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[