diff emboss_5/emboss_palindrome.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_5/emboss_palindrome.xml	Tue Dec 20 14:02:45 2011 -0500
@@ -0,0 +1,61 @@
+<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
+  <description>Looks for inverted repeats in a nucleotide sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="minpallen" size="4" type="text" value="10">
+      <label>Minimum length of palindrome</label>
+    </param>
+    <param name="maxpallen" size="4" type="text" value="100">
+      <label>Maximum length of palindrome</label>
+    </param>
+    <param name="gaplimit" size="4" type="text" value="100">
+      <label>Maximum gap between repeated regions</label>
+    </param>
+    <param name="nummismatches" size="4" type="text" value="0">
+      <label>Number of mismatches allowed</label>
+    </param>
+    <param name="overlap" type="select">
+      <label>Report overlapping matches</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="palindrome" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="minpallen" value="10"/>
+      <param name="maxpallen" value="100"/>
+      <param name="gaplimit" value="100"/>
+      <param name="nummismatches" value="0"/>
+      <param name="overlap" value="yes"/>
+      <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
+If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+  </help>
+</tool>