diff emboss_pepnet.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_pepnet.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,28 @@
+<tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0">
+  <!-- graphical output file with path information -->
+  <description>Displays proteins as a helical net</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic $amphipathic -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence" />
+    <param name="squares" type="text" value="ILVM" label="Residues to mark with squares" />
+    <param name="diamonds" type="text" value="DENQST" label="Residues to mark with diamonds" />
+    <param name="octags" type="text" value="HKR" label="Residues to mark with octagons" />
+    <param name="amphipathic" type="select" label="Amphipathic?" help="If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="png" />
+  </outputs>
+  <help>
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepnet.html
+  </help>
+  <expand macro="citations" />
+</tool>