Mercurial > repos > jjohnson > cummerbund

comparison cuffdiff_wrapper.xml @ 7:b5562b9a55c7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Use same bias_correction cached param as devteam cuffdiff
author Jim Johnson <jj@umn.edu>
date Mon, 13 Oct 2014 09:12:47 -0500
parents f109453ecfa2
children fbbbc9fd8fb9
comparison
equal deleted inserted replaced
6:137aab1d9ac1 7:b5562b9a55c7
38 #if $bias_correction.seq_source.index_source == "history": 38 #if $bias_correction.seq_source.index_source == "history":
39 ## Custom genome from history. 39 ## Custom genome from history.
40 $bias_correction.seq_source.ref_file 40 $bias_correction.seq_source.ref_file
41 #else: 41 #else:
42 ## Built-in genome. 42 ## Built-in genome.
43 ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')} 43 ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')}
44 #end if 44 #end if
45 #end if 45 #end if
46 46
47 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\'' 47 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
48 --labels $labels 48 --labels $labels
121 <conditional name="seq_source"> 121 <conditional name="seq_source">
122 <param name="index_source" type="select" label="Reference sequence data"> 122 <param name="index_source" type="select" label="Reference sequence data">
123 <option value="cached">Locally cached</option> 123 <option value="cached">Locally cached</option>
124 <option value="history">History</option> 124 <option value="history">History</option>
125 </param> 125 </param>
126 <when value="cached"></when> 126 <when value="cached">
127 <param name="index" type="select" label="Using reference genome">
128 <options from_data_table="fasta_indexes">
129 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
130 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
131 </options>
132 </param>
133 </when>
127 <when value="history"> 134 <when value="history">
128 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 135 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
129 </when> 136 </when>
130 </conditional> 137 </conditional>
131 </when> 138 </when>