--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shear_assemble.xml	Fri Nov 08 16:23:10 2013 -0500
@@ -0,0 +1,62 @@
+<tool id="shear_assemble" name="SHEAR-Assemble" version="0.0.5">
+  <description>create a personal genome from sdi</description>
+  <requirements>
+    <requirement type="package" version="0.2.5">shear</requirement>
+  </requirements>
+  <!--
+  <version_command></version_command>
+  -->
+  <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 $output_fasta
+  </command>
+  <inputs>
+    <param name="prefix" type="text" value="shear_assemble" label="Prefix for all generated files">
+      <validator type="regex" message="Prefix should start with a letter and contain only letter, digit, and '_' or '-' characters">[a-zA-Z0-9][_a-zA-Z0-9-]*</validator>
+    </param>
+    <param name="sdi_file" type="data" format="shear.sdi" label="SDI file produced by SHEAR's 'sv' command containing the SVs to use to create the new genomic sequence."/> 
+    <!-- reference data -->
+    <conditional name="genomeSource">
+      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
+        <option value="indexed">Use a cached reference genome</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="ref_fastas" type="select" label="Select a reference genome">
+          <options from_data_table="all_fasta">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No reference fasta files are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string}: ${prefix}.fa"  />
+  </outputs>
+  <tests>
+    <test>
+      <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" value="syn.fa" ftype="fasta" />
+      <output name="output_fasta"  file="simulated-data.fa"/>
+    </test>
+  </tests>
+  <help>
+SHEAR-Assemble takes a reference genome and a *.sdi file from SHEAR-SV to create a new personal genome.
+  </help>
+</tool>