Mercurial > repos > stemcellcommons > macs2
comparison macs2_wrapper.xml @ 20:db2805f9df66 draft
Replace simplejson with json.
| author | stemcellcommons |
|---|---|
| date | Wed, 09 Apr 2014 18:06:03 -0400 |
| parents | e047d7bbace9 |
| children | eed6c8dcef5d |
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| 19:e9c2c7d24e4e | 20:db2805f9df66 |
|---|---|
| 112 </data> | 112 </data> |
| 113 </outputs> | 113 </outputs> |
| 114 <configfiles> | 114 <configfiles> |
| 115 | 115 |
| 116 <configfile name="outputs_file"><% | 116 <configfile name="outputs_file"><% |
| 117 import simplejson | 117 import json |
| 118 %> | 118 %> |
| 119 ##======================================================================================= | 119 ##======================================================================================= |
| 120 #set $__outputs = { 'command':str( $major_command.major_command_selector ) } | 120 #set $__outputs = { 'command':str( $major_command.major_command_selector ) } |
| 121 #if str( $major_command.major_command_selector ) == 'callpeak': | 121 #if str( $major_command.major_command_selector ) == 'callpeak': |
| 122 #set $__outputs['output_bed_file'] = str( $output_bed_file ) | 122 #set $__outputs['output_bed_file'] = str( $output_bed_file ) |
| 130 ##======================================================================================= | 130 ##======================================================================================= |
| 131 #if str( $major_command.major_command_selector ) == 'bdgcmp': | 131 #if str( $major_command.major_command_selector ) == 'bdgcmp': |
| 132 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) | 132 #set $__outputs['output_bdgcmp_file'] = str( $output_bdgcmp_file ) |
| 133 #end if | 133 #end if |
| 134 | 134 |
| 135 ${ simplejson.dumps( __outputs ) } | 135 ${ json.dumps( __outputs ) } |
| 136 </configfile> | 136 </configfile> |
| 137 <configfile name="options_file"><% | 137 <configfile name="options_file"><% |
| 138 import simplejson | 138 import json |
| 139 %> | 139 %> |
| 140 ##======================================================================================= | 140 ##======================================================================================= |
| 141 #set $__options = { 'experiment_name':str( $experiment_name ) } | 141 #set $__options = { 'experiment_name':str( $experiment_name ) } |
| 142 ##treatment/tag input files and format | 142 ##treatment/tag input files and format |
| 143 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ] | 143 #set $__options['input_chipseq'] = [ str( $major_command.input_chipseq_file1 ) ] |
| 190 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) ) | 190 #set $__options['pseudocount'] = float( str( $major_command.pseudocount ) ) |
| 191 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector ) | 191 #set $__options['m'] = str( $major_command.bdgcmp_options.bdgcmp_options_selector ) |
| 192 #end if | 192 #end if |
| 193 ##======================================================================================= | 193 ##======================================================================================= |
| 194 | 194 |
| 195 ${ simplejson.dumps( __options ) } | 195 ${ json.dumps( __options ) } |
| 196 </configfile> | 196 </configfile> |
| 197 </configfiles> | 197 </configfiles> |
| 198 <tests> | 198 <tests> |
| 199 <!--none yet for macs2--> | 199 <!--none yet for macs2--> |
| 200 </tests> | 200 </tests> |