--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_trimest.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,92 @@
+<tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
+  <description>Trim poly-A tails off EST sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
+  -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="minlength" size="4" type="text" value="4">
+      <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
+    </param>
+    <param name="mismatches" size="4" type="text" value="1">
+      <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
+    </param>
+    <param name="reverse" type="select">
+      <label>Change the sequence to the forward sense when it is written out</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="tolower" type="select">
+      <label>Mask poly-A by converting to lowercase</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="fiveprime" type="select">
+      <label>Inspect 5' end of the sequence for poly-T tails</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Sequence File Format</label>
+      <option value="fasta">FASTA (m)</option>
+      <option value="acedb">ACeDB (m)</option>
+      <option value="asn1">ASN.1 (m)</option>
+      <option value="clustal">Clustal (m)</option>
+      <option value="codata">CODATA (m)</option>
+      <option value="embl">EMBL (m)</option>
+      <option value="fitch">Fitch (m)</option>
+      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
+      <option value="genbank">GENBANK (m)</option>
+      <option value="gff">GFF (m)</option>
+      <option value="hennig86">Hennig86 (m)</option>
+      <option value="ig">Intelligenetics (m)</option>
+      <option value="jackknifer">Jackknifer (m)</option>
+      <option value="jackknifernon">Jackknifernon (m)</option>
+      <option value="mega">Mega (m)</option>
+      <option value="meganon">Meganon (m)</option>
+      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
+      <option value="pir">NBRF (PIR) (m)</option>
+      <option value="ncbi">NCBI style FASTA (m)</option>
+      <option value="nexus">Nexus/PAUP (m)</option>
+      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
+      <option value="phylip">PHYLIP interleaved (m)</option>
+      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
+      <option value="selex">SELEX (m)</option>
+      <option value="staden">Staden (s)</option>
+      <option value="strider">DNA strider (m)</option>
+      <option value="swiss">SwisProt entry (m)</option>
+      <option value="text">Plain sequence (s)</option>
+      <option value="treecon">Treecon (m)</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fasta" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="minlength" value="4"/>
+      <param name="mismatches" value="1"/>
+      <param name="reverse" value="yes"/>
+      <param name="tolower" value="no"/>
+      <param name="fiveprime" value="yes"/>
+      <param name="out_format1" value="fasta"/>
+      <output name="out_file1" file="emboss_trimest_out.fasta"/>
+    </test>
+  </tests>
+  <code file="emboss_format_corrector.py" />
+  <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/trimest.html
+  </help>
+</tool>