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comparison getfastaBed.xml @ 40:a68aa6c1204a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
author iuc
date Thu, 09 Sep 2021 13:04:07 +0000
parents 3e38c9b3214f
children 7ab85ac5f64b
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39:3e38c9b3214f 40:a68aa6c1204a
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if str($fasta_source.fasta_source_selector) == 'history': 10 #if str($fasta_source.fasta_source_selector) == 'history':
11 #set $fasta_file = $fasta_source.fasta 11 #set $fasta_file = $fasta_source.fasta
12 #else 12 #else
13 #set $fasta_file = $fasta_source.fasta_id.fields.path 13 #set $fasta_file = $fasta_source.fasta_id.fields.path
14 ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
14 #end if 15 #end if
16 ln -s '$fasta_file' 'input.fasta' &&
15 bedtools getfasta 17 bedtools getfasta
16 $name 18 $name
17 $tab 19 $tab
18 $strand 20 $strand
19 $split 21 $split
20 -fi '$fasta_file' 22 -fi 'input.fasta'
21 -bed '$input' 23 -bed '$input'
22 -fo '$output' 24 -fo '$output'
23 ]]></command> 25 ]]></command>
24 <inputs> 26 <inputs>
25 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" /> 27 <param name="input" argument="-bed" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />