diff emboss_oddcomp.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_oddcomp.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,36 @@
+<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1">
+  <!-- output contains file location info, commented out functional tests -->
+  <description>Find protein sequence regions with a biased composition</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequences" />
+    <param name="input2" type="data" format="data" label="Dataset in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis" />
+    <param name="window" type="integer" value="30" label="Size of window in which to count" help="If you want to count frequencies in a 40 aa stretch you should enter 40 here" />
+    <param name="ignorebz" type="select" label="Ignore B and Z" help="The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="oddcomp" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="input2" value="emboss_compseq_out.compseq"/>
+      <param name="window" value="30"/>
+      <param name="ignorebz" value="yes"/>
+      <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
+    </test>
+  </tests> -->
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/oddcomp.html
+  </help>
+  <expand macro="citations" />
+</tool>