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comparison getfastaBed.xml @ 10:c78cf6fe3018 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
author iuc
date Mon, 03 Oct 2016 07:36:08 -0400
parents 607c0576c6ab
children 7308cc546a36
comparison
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9:2ab422b551df 10:c78cf6fe3018
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
28 <conditional name="fasta_source">
29 <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
30 <option value="history" selected="True">History</option>
31 <option value="preloaded">Server indexed files</option>
32 </param>
33 <when value="history">
34 <param name="fasta" format="fasta" type="data" label="Fasta file" />
35 </when>
36 <when value="preloaded">
37 <param name="fasta_id" type="select">
38 <options from_data_table="all_fasta" />
39 </param>
40 </when>
41 </conditional>
23 <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue="" 42 <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" 43 label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
25 help="(-name)" /> 44 help="(-name)" />
26 <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue="" 45 <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" 46 label="Report extract sequences in a tab-delimited format instead of in FASTA format"