Mercurial > repos > iuc > bedtools

diff slopBed.xml @ 17:44867b59dbf2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author iuc
date Tue, 05 Sep 2017 15:40:14 -0400
parents 7308cc546a36
children a8eabd2838f6
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--- a/slopBed.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/slopBed.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_slopbed" name="SlopBed" version="@WRAPPER_VERSION@.1">
     <description>adjust the size of intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -10,7 +10,7 @@
         bedtools slop
         $pct
         $strand
-        -g '$genome'
+        -g @GENOME_FILE@
         -i '$inputA'
         #if $addition.addition_select == 'b':
             -b $addition.b
@@ -24,7 +24,7 @@
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <expand macro="genome" />
+        <expand macro="input_conditional_genome_file" />
         <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue=""
             label="Define -l and -r as a fraction of the feature’s length"
             help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
@@ -40,6 +40,7 @@
     <tests>
         <test>
             <param name="inputA" value="a.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9_chr1.len" ftype="bed" />
             <param name="addition_select" value="b" />
             <param name="b" value="5" />
@@ -47,6 +48,7 @@
         </test>
         <test>
             <param name="inputA" value="a.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="mm9_chr1.len" ftype="bed" />
             <param name="addition_select" value="lr" />
             <param name="l" value="2" />