diff emboss_fuzznuc.xml @ 11:0e2484b6829b draft

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

--- a/emboss_fuzznuc.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_fuzznuc.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,53 +1,50 @@
-<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
-  <description>Nucleic acid pattern search</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
-  <inputs>
-    <param format="fasta" name="input1" type="data">
-      <label>Sequences</label>
-    </param>
-    <param name="pattern" type="text" value="">
-      <label>Search pattern</label>
-      <sanitizer>
-        <valid initial="string.printable">
-         <remove value="&apos;"/>
-        </valid>
-        <mapping initial="none">
-          <add source="&apos;" target=""/>
-        </mapping>
-      </sanitizer>
-    </param>
-    <param name="mismatch" type="text" value="0">
-      <label>Number of mismatches</label>
-    </param>
-    <param name="complement" type="select">
-      <label>Search complementary strand</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="out_format1" type="select">
-      <label>Output Report File Format</label>
-      <option value="seqtable">SeqTable</option>
-      <option value="embl">EMBL</option>
-      <option value="genbank">GENBANK</option>
-      <option value="gff">GFF</option>
-      <option value="pir">PIR</option>
-      <option value="swiss">SwissProt</option>
-      <option value="dbmotif">DbMotif</option>
-      <option value="diffseq">Diffseq</option>
-      <option value="excel">Excel (tab delimited)</option>
-      <option value="feattable">FeatTable</option>
-      <option value="motif">Motif</option>
-      <option value="regions">Regions</option>
+<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2">
+  <description>Nucleic acid pattern search</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="Sequences" />
+    <param name="pattern" type="text" value="" label="Search pattern">
+      <sanitizer>
+        <valid initial="string.printable">
+         <remove value="&apos;"/>
+        </valid>
+        <mapping initial="none">
+          <add source="&apos;" target=""/>
+        </mapping>
+      </sanitizer>
+    </param>
+    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
+    <param name="complement" type="select" label="Search complementary strand">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="out_format1" type="select" label="Output report file format">
+      <option value="seqtable">SeqTable</option>
+      <option value="embl">EMBL</option>
+      <option value="genbank">GENBANK</option>
+      <option value="gff">GFF</option>
+      <option value="pir">PIR</option>
+      <option value="swiss">SwissProt</option>
+      <option value="dbmotif">DbMotif</option>
+      <option value="diffseq">Diffseq</option>
+      <option value="excel">Excel (tab delimited)</option>
+      <option value="feattable">FeatTable</option>
+      <option value="motif">Motif</option>
+      <option value="regions">Regions</option>
       <option value="simple">SRS Simple</option>
-      <option value="fuzznuc">Fuzznuc Output File</option>
-      <option value="srs">SRS</option>
-      <option value="table">Table</option>
-      <option value="tagseq">TagSeq</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="fuzznuc" name="out_file1" />
+      <option value="fuzznuc">Fuzznuc Output File</option>
+      <option value="srs">SRS</option>
+      <option value="table">Table</option>
+      <option value="tagseq">TagSeq</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="fuzznuc" />
   </outputs>
   <tests>
     <test>
@@ -58,10 +55,8 @@
       <param name="out_format1" value="excel"/>
       <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
     </test>
-  </tests>
-  <code file="emboss_format_corrector.py" />
+  </tests>
   <help>
-
 .. class:: warningmark
 
 The input dataset needs to be sequences.
@@ -69,15 +64,8 @@
 -----
 
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.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;`_
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html
   </help>
+  <expand macro="citations" />
 </tool>