diff shear_assemble.xml @ 4:a82400332451

Use shear_wrapper.py to generate reference indexes when needed

--- a/shear_assemble.xml	Mon Jul 08 01:10:38 2013 -0500
+++ b/shear_assemble.xml	Tue Jul 16 12:38:48 2013 -0500
@@ -6,15 +6,21 @@
   <!--
   <version_command></version_command>
   -->
-  <command>java -jar \$SHEAR_JAR_PATH/SHEAR.jar assemble -s $sdi_file 
-     #if $genomeSource.refGenomeSource == 'indexed':
-       -f $genomeSource.ref_fastas.fields.path
-     #else:
-       -f $genomeSource.ref_fasta
-     #end if
-     -o $output_fasta
+  <command interpreter="python">
+    shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command assemble 
+    -p $prefix
+    -s $sdi_file
+    #if $genomeSource.refGenomeSource == 'indexed':
+      -f $genomeSource.ref_fastas.fields.path
+    #else:
+      -f $genomeSource.ref_fasta
+    #end if
+    -o $output_fasta
   </command>
   <inputs>
+    <param name="prefix" type="text" value="shear_assemble" label="Prefix for all generated files">
+      <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator>
+    </param>
     <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/> 
     <!-- reference data -->
     <conditional name="genomeSource">
@@ -39,13 +45,14 @@
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
   <outputs>
-    <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: personal genome"  />
+    <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: ${prefix}.fa"  />
   </outputs>
   <tests>
     <test>
-      <param name="sdi_file" ftype="shear.sdi" value="shear_sv.sdi"/>
+      <param name="prefix" value="shear_assembly" />
+      <param name="sdi_file" value="shear_sv.sdi" ftype="shear.sdi" />
       <param name="refGenomeSource" value="history"/>
-      <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
+      <param name="ref_fasta" value="syn.fa" ftype="fasta" />
       <output name="output_fasta"  file="simulated-data.fa"/>
     </test>
   </tests>