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comparison cuffdiff_wrapper.xml @ 2:2d6a90609943

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Fix wrapper bugs: (a) do not try update check and (b) allow spaces in labels.
author jeremy goecks <jeremy.goecks@emory.edu>
date Tue, 22 Oct 2013 11:03:02 -0400
parents 60a52f8460a1
children beab768feb92
comparison
equal deleted inserted replaced
1:60a52f8460a1 2:2d6a90609943
5 <requirement type="package" version="2.1.1">cufflinks</requirement> 5 <requirement type="package" version="2.1.1">cufflinks</requirement>
6 </requirements> 6 </requirements>
7 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command> 7 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
8 <command> 8 <command>
9 cuffdiff 9 cuffdiff
10 --no-update-check
10 --FDR=$fdr 11 --FDR=$fdr
11 --num-threads="4" 12 --num-threads="4"
12 --min-alignment-count=$min_alignment_count 13 --min-alignment-count=$min_alignment_count
13 --library-norm-method=$library_norm_method 14 --library-norm-method=$library_norm_method
14 --dispersion-method=$dispersion_method 15 --dispersion-method=$dispersion_method
34 ## Built-in genome. 35 ## Built-in genome.
35 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} 36 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
36 #end if 37 #end if
37 #end if 38 #end if
38 39
39 #set labels = ','.join( [ str( $condition.name ) for $condition in $conditions ] ) 40 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
40 --labels $labels 41 --labels $labels
41 42
42 ## Inputs. 43 ## Inputs.
43 $gtf_input 44 $gtf_input
44 #for $condition in $conditions: 45 #for $condition in $conditions: