diff emboss_cpgreport.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_cpgreport.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,57 @@
+<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0.1">
+  <description>Reports all CpG rich regions</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command><![CDATA[
+    cpgreport
+      -sequence '$input1'
+      -outfile '$out_file1'
+      -outfeat '$out_file2'
+      -offormat3 $out_format2
+      -score $score
+      -auto
+  ]]>
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="On query" />
+    <param name="score" type="integer" min="1" max="200" value="17" label="Score for each CG sequence found" />
+    <param name="out_format2" type="select" label="Output feature file format">
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="cpgreport" />
+    <data name="out_file2" format="gff" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="score" value="17"/>
+      <param name="out_format2" value="embl"/>
+      <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
+    </test>
+    <!-- <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="score" value="17"/>
+      <param name="out_format2" value="gff"/>
+      <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
+    </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/cpgreport.html
+  </help>
+  <expand macro="citations" />
+</tool>