diff gemini_pathways.xml @ 5:c63b7eefb07a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59

--- a/gemini_pathways.xml	Fri Dec 14 13:02:36 2018 -0500
+++ b/gemini_pathways.xml	Fri Jan 11 17:51:37 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
     <description>Map genes and variants to KEGG pathways</description>
     <macros>
         <import>gemini_macros.xml</import>
@@ -15,18 +15,23 @@
             @BINARY@
             -v $ensembl
             $lof
-            "${ infile }"
-            > "${ outfile }"
+            '$infile'
+            > '$outfile'
 ]]>
     </command>
     <inputs>
         <expand macro="infile" />
 
-        <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
-            help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
-            <validator type="in_range" min="66" max="71"/>
+        <param name="ensembl" type="select"
+        label="Version of ensembl genes to use"
+        help="Supported versions: 66 to 71. Use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
+            <option value="71">Ensembl 71</option>
+            <option value="70">Ensembl 70</option>
+            <option value="69">Ensembl 69</option>
+            <option value="68">Ensembl 68</option>
+            <option value="67">Ensembl 67</option>
+            <option value="66">Ensembl 66</option>
         </param>
-
         <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
             label="Report only pathways with loss-of-function variants" help="(--lof)"/>
         <expand macro="annotation_dir" />
@@ -37,7 +42,7 @@
     <tests>
         <test>
             <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
-            <param name="ensembl" value="68" />
+            <param name="ensembl" value="71" />
             <output name="outfile">
                 <assert_contents>
                     <has_line_matching expression="chrom&#009;start&#009;end&#009;.*pathway.*" />