diff emboss_5/emboss_newcpgreport.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_newcpgreport.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
+  <description>Report CpG rich areas</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
+  <inputs>
+    <param format="data" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="window" size="4" type="text" value="100">
+      <label>Window Size</label>
+    </param>
+    <param name="shift" size="4" type="text" value="1">
+      <label>Step size (shift)</label>
+    </param>
+    <param name="minlen" size="4" type="text" value="200">
+      <label>Minimum length</label>
+    </param>
+    <param name="minoe" size="4" type="text" value="0.6">
+      <label>Minimum average observed to expected ratio</label>
+    </param>
+    <param name="minpc" size="4" type="text" value="50.0">
+      <label>Minimum average percentage of G plus C</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="newcpgreport" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="window" value="100"/>
+      <param name="shift" value="1"/>
+      <param name="minlen" value="200"/>
+      <param name="minoe" value="0.6"/>
+      <param name="minpc" value="50.0"/>
+      <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/>
+    </test>
+  </tests>
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.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>
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