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comparison download_align.xml @ 28:e0e38389a9cb draft default tip

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author eduardo
date Tue, 04 Aug 2015 10:59:51 -0400
parents 8f36fc727988
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27:8f36fc727988 28:e0e38389a9cb
12 ln -s "$reference_genome.own_file" genome.fa && 12 ln -s "$reference_genome.own_file" genome.fa &&
13 #set index_path = 'genome' 13 #set index_path = 'genome'
14 #else: 14 #else:
15 #set index_path = $reference_genome.index.fields.path 15 #set index_path = $reference_genome.index.fields.path
16 #end if 16 #end if
17 wget -O - $file | gunzip -c | cutadapt -q 20 - | bowtie2 -q 17 wget -O - $file | gunzip -c | cutadapt -q 20 -m 20 - | bowtie2 -q
18 ## index file path 18 ## index file path
19 -x $index_path 19 -x $index_path
20 -U - | samtools view -b - > $output 20 -U - | samtools view -bS - > $output
21 </command> 21 </command>
22 <stdio> 22 <stdio>
23 <exit_code range="1:" level="fatal" description="Tool exception" /> 23 <exit_code range="1:" level="fatal" description="Tool exception" />
24 </stdio> 24 </stdio>
25 <inputs> 25 <inputs>