diff emboss_wordmatch.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_wordmatch.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,68 @@
+<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0.1">
+  <description>Finds all exact matches of a given size between 2 sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2
+  -offormat5 $out_format3 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence 1" />
+    <param name="input2" type="data" format="fasta" label="Sequence 2" />
+    <param name="wordsize" type="integer" value="4" label="Word size" />
+    <param name="out_format1" type="select" label="Output alignment file format">
+      <option value="match">Match (m)</option>
+      <option value="simple">Simple (m)</option>
+      <option value="fasta">FASTA (m)</option>
+      <option value="msf">MSF (m)</option>
+      <option value="srs">SRS (m)</option>
+      <option value="pair">Pair (p)</option>
+      <option value="markx0">Markx0 (p)</option>
+      <option value="markx1">Markx1 (p)</option>
+      <option value="markx2">Markx2 (p)</option>
+      <option value="markx3">Markx3 (p)</option>
+      <option value="markx10">Markx10 (p)</option>
+      <option value="srspair">SRS pair (p)</option>
+      <option value="score">Score (p)</option>
+    </param>
+    <param name="out_format2" type="select" label="Output feature 1 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="Output feature 2 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="match" />
+    <data name="out_file2" format="gff" />
+    <data name="out_file3" format="gff" />
+  </outputs>
+  <!--   <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="1.fasta"/>
+      <param name="wordsize" value="4"/>
+      <param name="out_format1" value="fasta"/>
+      <param name="out_format2" value="gff"/>
+      <param name="out_format3" value="gff"/>
+      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
+    </test>
+  </tests> test takes a long time to run-->
+  <help>
+.. class:: warningmark
+
+The input datasets need to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordmatch.html
+  </help>
+  <expand macro="citations" />
+</tool>