diff emboss_epestfind.xml @ 11:0e2484b6829b draft

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

--- a/emboss_epestfind.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_epestfind.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,48 +1,40 @@
-<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
-  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
-  -invalid $invalid -map $map -graph png -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>Sequence</label>
-    </param>
-    <param name="window" type="text" value="10">
-      <label>Minimal distance between positively charged amino acids</label>
-    </param>
-    <param name="order" type="select">
-      <label>Sort by</label>
-      <option value="3">Score</option>
-      <option value="1">Length</option>
-      <option value="2">Position</option>
-    </param>
-    <param name="threshold" type="text" value="5.0">
-      <label>Threshold value to discriminate weak from potential PEST motifs.</label>
-    </param>
-    <param name="potential" type="select">
-      <label>Decide whether potential PEST motifs should be printed</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <param name="poor" type="select">
-      <label>Decide whether poor PEST motifs should be printed</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-    <param name="invalid" type="select">
-      <label>Decide whether invalid PEST motifs should be printed</label>
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="map" type="select">
-      <label>Decide whether PEST motifs should be mapped to sequence</label>
-      <option value="yes">Yes</option>
-      <option value="no">No</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="png" name="ofile2" />
-    <data format="epestfind" name="ofile1" />
+<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1">
+  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
+  -invalid $invalid -map $map -graph png -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="Sequence" />
+    <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
+    <param name="order" type="select" label="Sort by">
+      <option value="3">Score</option>
+      <option value="1">Length</option>
+      <option value="2">Position</option>
+    </param>
+    <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
+    <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
+      <option value="no">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="ofile2" format="png" />
+    <data name="ofile1" format="epestfind" />
   </outputs>
 <!--    <tests>
     <test>
@@ -56,18 +48,11 @@
       <param name="map" value="yes"/>
       <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
     </test>
-  </tests>  output file contains file location info  -->
+  </tests>  output file contains file location info  -->
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.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/epestfind.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>