diff racon.xml @ 1:4df02149a270 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit da382e2ab73f0bb19ed85d74a338c47a43a0973a

--- a/racon.xml	Mon Jun 11 16:47:50 2018 -0400
+++ b/racon.xml	Thu Jul 19 07:43:14 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="racon" name="Racon" version="1.3.1">
+<tool id="racon" name="Racon" version="1.3.1.1">
     <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description>
     <macros>
         <import>macros.xml</import>
@@ -7,12 +7,20 @@
     <version_command>racon --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$reads' reads.${reads.ext} && 
-        ln -s '$overlaps' overlaps.${overlaps.ext} && 
+        #if $overlaps.ext == 'sam':
+            ln -s '$overlaps' overlaps.${overlaps.ext} && 
+        #else:
+            ln -s '$overlaps' overlaps.paf &&
+        #end if
         ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && 
 
         racon 
-            reads.${reads.ext}  
-            overlaps.${overlaps.ext}  
+            reads.${reads.ext}
+            #if $overlaps.ext == 'sam':
+                overlaps.${overlaps.ext}
+            #else:
+                overlaps.paf
+            #end if
             corrected_reads.${corrected_reads.ext}
             -t \${GALAXY_SLOTS:-4} 
             $u
@@ -27,7 +35,7 @@
     ]]></command>
     <inputs>
         <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/>
-        <param type="data" name="overlaps" format="sam" label="Overlaps"/>
+        <param type="data" name="overlaps" format="sam,interval" label="Overlaps"/>
         <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/>
 
         <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" />
@@ -54,6 +62,12 @@
             <param name="e" value="0.2"/>
             <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/>
         </test>
+        <test>
+            <param name="reads" ftype="fasta" value="sample_reads.fasta"/>
+            <param name="overlaps" ftype="interval" value="sample_overlaps.paf"/>
+            <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/>
+            <output name="consensus" ftype="fasta" file="consensus_result3.fasta"/>
+        </test>
     </tests>
     <help><![CDATA[