diff emboss_cpgreport.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

--- a/emboss_cpgreport.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_cpgreport.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,65 +1,57 @@
-<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>
+<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>