diff shear_sv.xml @ 4:a82400332451

Use shear_wrapper.py to generate reference indexes when needed

--- a/shear_sv.xml	Mon Jul 08 01:10:38 2013 -0500
+++ b/shear_sv.xml	Tue Jul 16 12:38:48 2013 -0500
@@ -11,27 +11,38 @@
   <!--
   <version_command></version_command>
   -->
-  <command>java -jar  \$SHEAR_JAR_PATH/SHEAR.jar sv -p $prefix 
-     -b $bamfile 
+  <command interpreter="python">
+    shear_wrapper.py -j \$SHEAR_JAR_PATH/SHEAR.jar --command sv 
+    -p $prefix 
+    -b $bamfile 
      #if $genomeSource.refGenomeSource == 'indexed':
        -f $genomeSource.ref_fastas.fields.path 
        -i $genomeSource.bwa_indices.fields.path 
        -t $genomeSource.twobit_indices.fields.path
+     #elif $genomeSource.refGenomeSource == 'svidx':
+       -f $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
+       -i $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.fa
+       -t $genomeSource.svidx.extra_files_path/${genomeSource.svidx.metadata.base_name}.2bit
      #else:
        -f $genomeSource.ref_fasta
-       -i $genomeSource.bwa_index
-       -t $genomeSource.twobit
+       #if $genomeSource.save_svidx:
+         -D $sv_idx.extra_files_path
+       #end if
      #end if
+     --report $report
+     --sdi $sdi
   </command>
   <inputs>
     <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> 
+    <param name="prefix" type="text" value="shear_sv" 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>
     <!-- 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" selected="true">Use a cached reference genome</option>
-        <!--
-        <option value="history">Use one from the history</option>
-        -->
+        <option value="history">Use fasta from the history</option>
+        <option value="svidx">Use SHEAR sv index from the history</option>
       </param>
       <when value="indexed">
         <param name="ref_fastas" type="select" label="Select a reference genome fasta">
@@ -59,31 +70,32 @@
           </options>
         </param>
       </when>
-      <!--
       <when value="history">
-        <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
-        <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" />
-        <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+        <param name="ref_fasta" type="data" format="fasta" label="Select a reference from history" />
+        <param name="save_svidx" type="boolean" truevalue="yes" falsevalue="no" label="Save sv generated reference indexes"/> 
       </when>
-      -->
+      <when value="svidx">
+        <param name="svidx" type="data" format="shear.svidx" label="Select a reference from history" />
+      </when>
     </conditional>
-    <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
   </inputs>
   <stdio>
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
   <outputs>
-    <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: shear_sv.sdi" from_work_dir="shear_sv.sdi" />
-    <data format="txt" name="report" label="${tool.name} on ${on_string}: shear_sv.report" from_work_dir="shear_sv.report"/>
+    <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: ${prefix}.sdi" />
+    <data format="txt" name="report" label="${tool.name} on ${on_string}: ${prefix}.report" />
+    <data format="shear.svidx" name="sv_idx" label="${tool.name} on ${on_string}: ${prefix}.svidx">
+      <filter>genomeSource['refGenomeSource'] == 'history' and genomeSource['save_svidx'] == True</filter>
+    </data>
   </outputs>
   <tests>
     <test>
-      <param name="bamfile" ftype="bam" value="simulated-data.bam"/>
+      <param name="prefix" value="shear_test" />
+      <param name="bamfile" value="simulated-data.bam" ftype="bam" />
       <param name="refGenomeSource" value="history"/>
-      <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
-      <param name="bwa_index" ftype="" value="syn.fa"/>
-      <param name="twobit" ftype="twobit" value="syn.2bit"/>
-      <output name="shear.sdi"  file="shear_sv.sdi"/>
+      <param name="ref_fasta" value="syn.fa" ftype="fasta" />
+      <output name="sdi"  file="shear_sv.sdi"/>
       <output name="report"  file="shear_sv.report"/>
     </test>
   </tests>