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comparison annotateBed.xml @ 18:5efc48568d8d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:20:34 -0400
parents a2d4c30ba2f9
children c0fbce5dc84a
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17:a2d4c30ba2f9 18:5efc48568d8d
1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.1">
2 <description>annotate coverage of features from multiple files</description> 2 <description>annotate coverage of features from multiple files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10
10 bedtools annotate 11 bedtools annotate
11 -i "${inputA}" 12 -i "${inputA}"
12 #if $names.names_select == 'yes': 13 #if $names.names_select == 'yes':
13 -files 14 -files
14 #for $bed in $names.beds: 15 #for $bed in $names.beds:
20 "${bed.inputName}" 21 "${bed.inputName}"
21 #end for 22 #end for
22 #else: 23 #else:
23 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] ) 24 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
24 -files "${files}" 25 -files "${files}"
26 #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
27 -names "${names}"
25 #end if 28 #end if
26 $strand 29 $strand
27 $counts 30 $counts
28 $both 31 $both
29 > "${output}" 32 > "${output}"