diff tools/rtg/snp.xml @ 1:8593828f91e7 default tip

Full galaxy wrapper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rtg/snp.xml	Sat Apr 21 21:36:15 2012 -0400
@@ -0,0 +1,37 @@
+<tool id="rtg_snp" name="Call SNPs">
+  <description>from SAM files with rtg snp</description>
+  <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ snps.vcf
+snp -t ${template.extra_files_path} 
+--max-as-mated $maxscore
+--max-as-unmated $maxuscore
+--machine-errors $machine
+$input1
+#for $i in $inputs
+  ${i.input}
+#end for
+-Z
+</command>
+  <inputs>
+    <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
+    <param name="maxscore" type="integer" value="3" label="Maximum alignment score for mated reads"/>
+    <param name="maxuscore" type="integer" value="1" label="Maximum alignment score for umated reads"/>
+    <param name="machine" type="select" label="Select machine type">
+      <option value="illumina">Illumina</option>
+      <option value="cg">Complete Genomics</option>
+      <option value="454_se">454 single-end</option>
+      <option value="454_pe">454 paired-end</option>
+    </param>
+    <param name="input1" label="First tabix-ed SAM file" type="data" format="samix" />
+    <repeat name="inputs" title="Input tabix-ed SAM Files">
+      <param name="input" label="Add file" type="data" format="samix" />
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="output" format="vcf" />
+  </outputs>
+
+  <help>
+This tool calls snps from SAM files
+  </help>
+
+</tool>