diff tools/emboss_5/emboss_equicktandem.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/emboss_5/emboss_equicktandem.xml	Fri Mar 09 19:37:19 2012 -0500
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+<tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
+  <description>Finds tandem repeats</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>Sequence</label>
+    </param>
+    <param name="maxrepeat" size="4" type="text" value="600">
+      <label>Maximum repeat size</label>
+    </param>
+    <param name="threshold" size="4" type="text" value="20">
+      <label>Threshold score</label>
+    </param>
+    <param name="out_format1" type="select">
+      <label>Output Report File Format</label>
+      <option value="table">Table</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
+      <option value="seqtable">SeqTable</option>
+      <option value="simple">SRS Simple</option>
+      <option value="srs">SRS</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="table" name="out_file1" />
+    <data format="equicktandem" name="ofile2" />
+  </outputs>
+    <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="maxrepeat" value="600"/>
+      <param name="threshold" value="20"/>
+      <param name="out_format1" value="table"/>
+      <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
+    </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/equicktandem.html
+  </help>
+</tool>