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diff emboss_diffseq.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
parents
children 8992d258e42f
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_diffseq.xml	Wed Feb 08 12:42:22 2017 -0500
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+<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0.1">
+  <description>Find differences between nearly identical sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
+  $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence 1" />
+    <param name="input2" type="data" format="data" label="Sequence 2" />
+    <param name="wordsize" type="integer" value="20" label="Wordsize" />
+    <param name="globaldifferences" type="select" label="Report differences at the ends">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <option value="diffseq">Diffseq</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="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="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+    <param name="out_format2" type="select" label="Sequence 1 output feature file format">
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+    <param name="out_format3" type="select" label="Sequence 2 output feature file format">
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="diffseq" />
+    <data name="out_file2" format="gff" />
+    <data name="out_file3" format="gff" />
+  </outputs>
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/diffseq.html
+  </help>
+  <expand macro="citations" />
+</tool>