diff tools/emboss_5/emboss_primersearch.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_primersearch.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,33 @@
+<tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
+  <description>Searches DNA sequences for matches with primer pairs</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Main sequences</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Primer file</label>
+    </param>
+    <param name="mismatchpercent" size="4" type="text" value="0">
+      <label>Allowed percent mismatch</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="primersearch" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="emboss_primersearch.fasta"/>
+      <param name="mismatchpercent" value="0"/>
+      <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
+    </test>
+  </tests>
+  <help>
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
+  </help>
+</tool>