diff bedToBam.xml @ 32:b0d5e752c0c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348

--- a/bedToBam.xml	Fri Aug 18 15:32:52 2017 -0400
+++ b/bedToBam.xml	Tue Sep 05 09:51:56 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_bedtobam" name="BED to BAM" version="@WRAPPER_VERSION@.1">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         bedtools bedtobam
         $bed12
         -mapq $mapq
-        -g $genome
+        -g @GENOME_FILE@
         -i '$input'
         > '$output'
 ]]>
@@ -20,7 +20,7 @@
         <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
             label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
             help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
-        <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)"/>
     </inputs>
@@ -30,6 +30,7 @@
     <tests>
         <test>
             <param name="input" value="bedToBam1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9_chr1.len" ftype="tabular" />
             <output name="output" file="bedToBam_result.bam" lines_diff="4" ftype="bam" />
         </test>