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comparison cuffdiff_wrapper.xml @ 1:60a52f8460a1

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Fix bias correction.
author jeremy goecks <jeremy.goecks@emory.edu>
date Wed, 09 Oct 2013 12:49:03 -0400
parents 0dabb2ed6eb1
children 2d6a90609943
comparison
equal deleted inserted replaced
0:0dabb2ed6eb1 1:60a52f8460a1
24 -u 24 -u
25 #end if 25 #end if
26 26
27 ## Bias correction? 27 ## Bias correction?
28 #if $bias_correction.do_bias_correction == "Yes": 28 #if $bias_correction.do_bias_correction == "Yes":
29 -b 29 -b
30 #if $bias_correction.seq_source.index_source == "history": 30 #if $bias_correction.seq_source.index_source == "history":
31 --ref_file=$bias_correction.seq_source.ref_file 31 ## Custom genome from history.
32 $bias_correction.seq_source.ref_file
32 #else: 33 #else:
33 --ref_file="None" 34 ## Built-in genome.
35 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
34 #end if 36 #end if
35 --dbkey=${gtf_input.metadata.dbkey}
36 --index_dir=${GALAXY_DATA_INDEX_DIR}
37 #end if 37 #end if
38 38
39 #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] ) 39 #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] )
40 --labels $labels 40 --labels $labels
41 41
114 </when> 114 </when>
115 </conditional> 115 </conditional>
116 </inputs> 116 </inputs>
117 117
118 <stdio> 118 <stdio>
119 <regex match="Error" source="both" level="fatal" description="Error"/>
119 <regex match=".*" source="both" level="log" description="tool progress"/> 120 <regex match=".*" source="both" level="log" description="tool progress"/>
120 </stdio> 121 </stdio>
121 122
122 <outputs> 123 <outputs>
123 <!-- Optional read group datasets. --> 124 <!-- Optional read group datasets. -->