Mercurial > repos > devteam > tophat_fusion_post
comparison tophat_fusion_post.xml @ 10:33aafd74bb31
Fix bugs: (a) use value rather than dbkey to get bowtie indices and (b) point to correct bowtie table.
author | devteam@galaxyproject.org |
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date | Thu, 27 Feb 2014 14:58:22 -0500 |
parents | 7d6658b2531a |
children | 08f88205d596 |
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9:7d6658b2531a | 10:33aafd74bb31 |
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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=""/> |