diff emboss_polydot.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_polydot.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,44 @@
+<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1">
+  <!-- produces png file, not added functional tests -->
+  <description>Displays all-against-all dotplots of a set of sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
+  $gap -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequence" />
+    <param name="wordsize" type="integer" value="6" label="Word size" />
+    <param name="boxit" type="select" label="Draw a box around each dotplot">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="gap" type="integer" value="10" label="Size of gap" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="polydot" />
+    <data name="output2" format="png" />
+  </outputs>
+<!--    <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="wordsize" value="6"/>
+      <param name="boxit" value="yes"/>
+      <param name="gap" value="10"/>
+      <output name="output1" file="emboss_polydot_out.png"/>
+    </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/polydot.html
+  </help>
+  <expand macro="citations" />
+</tool>