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comparison getfastaBed.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children da6d7bc0a8b0
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25:6c6963cf9136 26:c0fbce5dc84a
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 #if str( $fasta_source.fasta_source_selector ) == 'history':
11 #set $fasta_file = $fasta_source.fasta
12 #else
13 #set $fasta_file = $fasta_source.fasta_id.fields.path
14 #end if
10 bedtools getfasta 15 bedtools getfasta
11 $name 16 $name
12 $tab 17 $tab
13 $strand 18 $strand
14 $split 19 $split
15 -fi $fasta 20 -fi '$fasta_file'
16 -bed $input 21 -bed '$input'
17 -fo $output 22 -fo '$output'
18 ]]> 23 ]]>
19 </command> 24 </command>
20 <inputs> 25 <inputs>
21 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" /> 26 <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
22 <param format="fasta" name="fasta" type="data" label="Fasta file" /> 27 <conditional name="fasta_source">
28 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
29 <option value="history" selected="True">History</option>
30 <option value="preloaded">Server indexed files</option>
31 </param>
32 <when value="history">
33 <param name="fasta" format="fasta" type="data" label="Fasta file" />
34 </when>
35 <when value="preloaded">
36 <param name="fasta_id" type="select">
37 <options from_data_table="all_fasta" />
38 </param>
39 </when>
40 </conditional>
23 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" 41 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
24 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" 42 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
25 help="(-name)" /> 43 help="(-name)" />
26 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" 44 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
27 label="Report extract sequences in a tab-delimited format instead of in FASTA format" 45 label="Report extract sequences in a tab-delimited format instead of in FASTA format"