diff emboss_einverted.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_einverted.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,42 @@
+<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0.1">
+  <description>Finds DNA inverted repeats</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="On query" />
+    <param name="gap" type="integer" value="12" label="Gap penalty" />
+    <param name="threshold" type="integer" value="50" label="Minimum score threshold" />
+    <param name="match" type="integer" value="3" label="Match score" />
+    <param name="mismatch" type="integer" value="-4" label="Mismatch score" />
+    <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" />
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="einverted" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="1.fasta"/>
+      <param name="gap" value="12"/>
+      <param name="threshold" value="50"/>
+      <param name="match" value="3"/>
+      <param name="mismatch" value="-4"/>
+      <param name="maxrepeat" value="2000"/>
+      <output name="out_file1" file="emboss_einverted_out.einverted"/>
+    </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/einverted.html
+  </help>
+  <expand macro="citations" />
+</tool>