diff emboss_cpgreport.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_cpgreport.xml	Fri Aug 12 19:17:10 2016 -0400
@@ -0,0 +1,65 @@
+<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
+  <description>Reports all CpG rich regions</description>
+  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
+  <command><![CDATA[
+    cpgreport 
+      -sequence '$input1' 
+      -outfile '$out_file1' 
+      -outfeat '$out_file2'
+      -offormat3 '$out_format2'
+      -score '$score'
+      -auto
+  ]]>
+  </command>
+  <inputs>
+    <param format="fasta" name="input1" type="data">
+      <label>On query</label>
+    </param>
+    <param name="score" type="text" value="17">
+      <label>Score for each CG sequence found (1-200)</label>
+    </param>
+    <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 format="cpgreport" name="out_file1" />
+    <data format="gff" name="out_file2" />
+  </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>
+  <code file="emboss_format_corrector.py" />
+  <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/cpgreport.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>