diff bedpeToBam.xml @ 17:44867b59dbf2 draft

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

--- a/bedpeToBam.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/bedpeToBam.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_bedpetobam" name="BEDPE to BAM" version="@WRAPPER_VERSION@.1">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -10,13 +10,13 @@
         bedtools bedpetobam
             -mapq $mapq
             -i '$input'
-            -g $genome
+            -g @GENOME_FILE@
             > '$output'
 ]]>
     </command>
     <inputs>
         <param name="input" format="bed,gff,vcf" type="data" label="BED/VCF/GFF file"/>
-        <expand macro="genome" />
+        <expand macro="input_conditional_genome_file" />
         <param name="mapq" type="integer" value="255"
             label="Set a mapping quality (SAM MAPQ field) value for all BED entries"
             help="(-mapq)" />
@@ -27,6 +27,7 @@
     <tests>
         <test>
             <param name="input" value="bedpeToBamBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9.len"/>
             <output name="output" file="bedpeToBam_result1.bam" lines_diff="72" ftype="bam" />
         </test>