Mercurial > repos > devteam > freebayes
comparison freebayes.xml @ 22:99684adf84de draft
planemo upload commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
| author | devteam |
|---|---|
| date | Fri, 09 Oct 2015 17:20:08 -0400 |
| parents | 978760187fe2 |
| children | 52aed7d9ed2b |
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| 21:978760187fe2 | 22:99684adf84de |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="freebayes" name="FreeBayes" version="0.4"> | 2 <tool id="freebayes" name="FreeBayes" version="0.4.1"> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0_9_20_b040236">freebayes</requirement> | 4 <requirement type="package" version="0_9_20_b040236">freebayes</requirement> |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | 5 <requirement type="package" version="0.1.18">samtools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <description> - bayesian genetic variant detector</description> | 7 <description> - bayesian genetic variant detector</description> |
| 78 ## Command line direct text entry is not allowed at this time for security reasons | 78 ## Command line direct text entry is not allowed at this time for security reasons |
| 79 | 79 |
| 80 #elif str( $options_type.options_type_selector ) == "full": | 80 #elif str( $options_type.options_type_selector ) == "full": |
| 81 | 81 |
| 82 #if $options_type.optional_inputs.optional_inputs_selector: | 82 #if $options_type.optional_inputs.optional_inputs_selector: |
| 83 | 83 |
| 84 ${options_type.optional_inputs.report_monomorphic} | |
| 85 | |
| 84 #if $options_type.optional_inputs.output_trace_option: | 86 #if $options_type.optional_inputs.output_trace_option: |
| 85 --trace "${output_trace}" | 87 --trace "${output_trace}" |
| 86 #end if | 88 #end if |
| 87 | 89 |
| 88 #if $options_type.optional_inputs.output_failed_alleles_option: | 90 #if $options_type.optional_inputs.output_failed_alleles_option: |
| 120 | 122 |
| 121 #end if | 123 #end if |
| 122 | 124 |
| 123 ## REPORTING | 125 ## REPORTING |
| 124 | 126 |
| 125 ${options_type.optional_inputs.report_monomorphic} | |
| 126 | 127 |
| 127 #if str( $options_type.reporting.reporting_selector ) == "True": | 128 #if str( $options_type.reporting.reporting_selector ) == "True": |
| 128 --pvar ${options_type.reporting.pvar} | 129 --pvar ${options_type.reporting.pvar} |
| 129 #end if | 130 #end if |
| 130 | 131 |