diff emboss_5/emboss_supermatcher.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_5/emboss_supermatcher.xml	Tue Dec 20 14:02:45 2011 -0500
@@ -0,0 +1,72 @@
+<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
+  <!-- puts file information in output report -->
+  <description>Match large sequences against one or more other sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
+  $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Large sequences</label>
+    </param>
+    <param format="data" name="input2" type="data">
+      <label>Sequences to match</label>
+    </param>
+    <param name="gapopen" size="4" type="text" value="10.0">
+      <label>Gap opening penalty</label>
+    </param>
+    <param name="gapextend" size="4" type="text" value="0.5">
+      <label>Gap extension penalty</label>
+    </param>
+    <param name="width" size="4" type="text" value="16">
+      <label>Alignment width</label>
+    </param>
+    <param name="wordlen" size="4" type="text" value="6">
+      <label>Word length for initial matching</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Alignment File Format</label>
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="simple" name="ofile1" />
+    <data format="supermatcher" name="ofile2" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="gapopen" value="10.0"/>
+      <param name="gapextend" value="0.5"/>
+      <param name="width" value="16"/>
+      <param name="wordlen" value="6"/>
+      <param name="out_format1" value="fasta"/>
+      <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
+    </test>
+  </tests> -->
+  <code file="emboss_format_corrector.py" />
+  <help>
+    You can view the original documentation here_.
+    
+    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.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>