diff emboss_einverted.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_einverted.xml	Fri Aug 12 19:17:10 2016 -0400
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+<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
+  <description>Finds DNA inverted repeats</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param name="gap" type="text" value="12">
+      <label>Gap penalty</label>
+    </param>
+    <param name="threshold" type="text" value="50">
+      <label>Minimum score threshold</label>
+    </param>
+    <param name="match" type="text" value="3">
+      <label>Match score</label>
+    </param>
+    <param name="mismatch" type="text" value="-4">
+      <label>Mismatch score</label>
+    </param>
+    <param name="maxrepeat" type="text" value="2000">
+      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="einverted" name="out_file1" />
+  </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://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
+
+If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+  </help>
+</tool>