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comparison tophat_fusion_post.xml @ 10:33aafd74bb31

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Fix bugs: (a) use value rather than dbkey to get bowtie indices and (b) point to correct bowtie table.
author devteam@galaxyproject.org
date Thu, 27 Feb 2014 14:58:22 -0500
parents 7d6658b2531a
children 08f88205d596
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9:7d6658b2531a 10:33aafd74bb31
25 #if str($is_human) == 'No': 25 #if str($is_human) == 'No':
26 --non-human 26 --non-human
27 #end if 27 #end if
28 28
29 ## Bowtie indices. 29 ## Bowtie indices.
30 ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} 30 ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')}
31 </command> 31 </command>
32 32
33 <inputs> 33 <inputs>
34 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/> 34 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
35 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/> 35 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>