diff fisherBed.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

--- a/fisherBed.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/fisherBed.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_fisher" name="FisherBed" version="@WRAPPER_VERSION@.1">
     <description>calculate Fisher statistic between two feature files</description>
     <macros>
         <import>macros.xml</import>
@@ -13,7 +13,7 @@
         -a '$inputA'
         -b '$inputB'
         -f $overlap
-        -g $genome
+        -g @GENOME_FILE@
         $reciprocal
         $m
         > '$output'
@@ -22,7 +22,7 @@
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
         <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/>
-        <expand macro="genome" />
+        <expand macro="input_conditional_genome_file" />
         <expand macro="strand2" />
         <expand macro="split" />
         <expand macro="overlap" />
@@ -37,6 +37,7 @@
         <test>
             <param name="inputA" value="fisherBed1.bed" ftype="bed" />
             <param name="inputB" value="fisherBed2.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="fisherBed.len" ftype="tabular" />
             <output name="output" file="fisherBed_result1.bed" ftype="bed" />
         </test>