diff emboss_etandem.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_etandem.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,69 @@
+<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0.1">
+  <description>Looks for tandem repeats in a nucleotide sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence" />
+    <param name="minrepeat" type="integer" value="10" label="Minimum repeat size" />
+    <param name="maxrepeat" type="integer" value="10" label="Maximum repeat size" />
+    <param name="threshold" type="integer" value="20" label="Threshold score" />
+    <param name="mismatch" type="select" label="Allow N as a mismatch">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="uniform" type="select" label="Allow uniform consensus">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <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 name="out_file1" format="etandem" />
+    <data name="ofile2" format="table" />
+  </outputs>
+    <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="minrepeat" value="10"/>
+      <param name="maxrepeat" value="10"/>
+      <param name="threshold" value="20"/>
+      <param name="mismatch" value="no"/>
+       <param name="uniform" value="no"/>
+      <param name="out_format1" value="table"/>
+      <output name="ofile2" file="emboss_etandem_out.table"/>
+    </test>
+  </tests>
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/etandem.html
+  </help>
+  <expand macro="citations" />
+</tool>