diff emboss_5/emboss_trimseq.xml @ 0:b94ca591877b

Uploaded emboss_5.tar

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+++ b/emboss_5/emboss_trimseq.xml	Tue Dec 20 14:02:45 2011 -0500
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+<tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
+  <description>Trim ambiguous bits off the ends of sequences</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequences</label>
+    </param>
+    <param name="window" size="4" type="text" value="1">
+      <label>Window size</label>
+    </param>
+    <param name="percent" size="5" type="text" value="100.0">
+      <label>Threshold of the percentage ambiguity</label>
+    </param>
+    <param name="strict" type="select">
+      <label>Trim all ambiguity codes</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="star" type="select">
+      <label>In protein sequences, trim off not only X's, but also the *'s</label>
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="left" type="select">
+      <label>Trim at the start</label>
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="right" type="select">
+      <label>Trim at the end</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="window" value="1"/>
+      <param name="percent" value="100.0"/>
+      <param name="strict" value="no"/>
+      <param name="star" value="no"/>
+      <param name="left" value="yes"/>
+      <param name="right" value="yes"/>
+      <param name="out_format1" value="fasta"/>
+      <output name="out_file1" file="emboss_trimseq_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/trimseq.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>