diff emboss_5/emboss_compseq.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_compseq.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
+  <description>Count composition of dimer/trimer/etc words in a sequence</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param name="word" size="4" type="text" value="2">
+      <label>Size of word (window) to count</label>
+    </param>
+    <param name="frame" type="select">
+      <label>Frame to inspect</label>
+      <option value="0">All Frames</option>
+      <option value="1">Frame 1</option>
+      <option value="2">Frame 2</option>
+      <option value="3">Frame 3</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="compseq" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="word" value="2"/>
+      <param name="frame" value="0"/>
+      <output name="out_file1" file="emboss_compseq_out.compseq"/>
+    </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/compseq.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>