diff emboss_palindrome.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_palindrome.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,45 @@
+<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0.1">
+  <description>Looks for inverted repeats in a nucleotide sequence</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" />
+    <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" />
+    <param name="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" />
+    <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" />
+    <param name="overlap" type="select" label="Report overlapping matches">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="palindrome" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="minpallen" value="10"/>
+      <param name="maxpallen" value="100"/>
+      <param name="gaplimit" value="100"/>
+      <param name="nummismatches" value="0"/>
+      <param name="overlap" value="yes"/>
+      <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
+    </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/palindrome.html
+  </help>
+  <expand macro="citations" />
+</tool>