diff sspace.xml @ 1:93fa7ecb5292 draft

Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .

--- a/sspace.xml	Tue Sep 17 09:41:18 2013 -0400
+++ b/sspace.xml	Fri Feb 21 04:17:55 2014 -0500
@@ -1,21 +1,20 @@
-<tool id="sspace" name="SSPACE" version="1.0.5">
+<tool id="sspace" name="SSPACE" version="1.0.6">
   <description>scaffolder</description>
   <requirements>
     <requirement type="package" version="2.0">sspace</requirement>
   </requirements>
 
-  <command interpreter="python">
-    sspace.py
-    \${SSPACE_SITE_OPTIONS:--T 1}
-    -c $contigs --r1 $reads1 --r2 $reads2 -i $insert -e $error -o $orientation
+  <command>
+    echo "lib1 $reads1 $reads2 $insert $error $orientation" &gt; libraryfile &amp;&amp;
+    perl `which SSPACE_Basic_v2.0.pl` -l libraryfile -s $contigs
     #if $exten
-      -x
+      -x 1
     #end if
     #if str($minoverlap)
-      --minoverlap $minoverlap
+      -m $minoverlap
     #end if
     #if str($numofreads)
-      --numofreads $numofreads
+      -o $numofreads
     #end if
     #if str($max_trim)
       -t $max_trim
@@ -27,18 +26,18 @@
       -r $min_base_ratio
     #end if
     #if str($minlink)
-      --minlink $minlink
+      -k $minlink
     #end if
     #if str($maxratio)
-      --maxratio $maxratio
+      -a $maxratio
     #end if
     #if str($contigoverlap)
-      --contigoverlap $contigoverlap
+      -n $contigoverlap
     #end if
     #if str($mincontig)
-      --mincontig $mincontig
+      -z $mincontig
     #end if
-    --lib $libraryname --fe $finalevidence --fs $finalscaffolds --lg $logfile --summ $summaryfile
+    -T \${GALAXY_SLOTS:-1} -b sspace
   </command>
 
   <inputs>
@@ -78,11 +77,10 @@
   </inputs>
 
   <outputs>
-    <data name="libraryname" hidden="True" format="tabular" label="${tool.name} on ${on_string}: libraryfile" />
-    <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" />
-    <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" />
-    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
-    <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" />
+    <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" from_work_dir="sspace.final.evidence" />
+    <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" from_work_dir="sspace.final.scaffolds.fasta" />
+    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="sspace.logfile.txt" />
+    <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" from_work_dir="sspace.summaryfile.txt" />
   </outputs>
   <tests>