Mercurial > repos > greg > gene_family_integrator
comparison gene_family_integrator.xml @ 19:1dee3b4be156 draft
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| author | greg |
|---|---|
| date | Mon, 22 May 2017 15:22:01 -0400 |
| parents | 57f27f72c771 |
| children | b08f999574db |
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| 18:2aef84b19da6 | 19:1dee3b4be156 |
|---|---|
| 53 <expand macro="param_orthogroup_fna" /> | 53 <expand macro="param_orthogroup_fna" /> |
| 54 </when> | 54 </when> |
| 55 </conditional> | 55 </conditional> |
| 56 </inputs> | 56 </inputs> |
| 57 <outputs> | 57 <outputs> |
| 58 <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}"> | 58 <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}"> |
| 59 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> | 59 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> |
| 60 </data> | 60 </data> |
| 61 <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}"> | 61 <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters and corresponding coding sequences) on ${on_string}"> |
| 62 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter> | 62 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter> |
| 63 </data> | 63 </data> |
| 64 </outputs> | 64 </outputs> |
| 65 <tests> | 65 <tests> |
| 66 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. | |
| 67 <test> | 66 <test> |
| 67 <param name="input_format" value="ptorthocs"/> | |
| 68 <param name="input_ptorthocs" value="input.ptorthocs" ftype="ptorthocs"/> | |
| 69 <param name="scaffold" value="22Gv1.1"/> | |
| 70 <param name="method" value="orthomcl"/> | |
| 71 <param name="classifier" value="both"/> | |
| 72 <param name="orthogroup_fna" value="yes"/> | |
| 73 <output name="output_ptorthocs" file="output.ptorthocs" ftype="ptorthocs"/> | |
| 68 </test> | 74 </test> |
| 69 --> | |
| 70 </tests> | 75 </tests> |
| 71 <help> | 76 <help> |
| 72 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary | 77 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary |
| 73 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone | 78 analyses of genome-scale gene families and transcriptomes. This tool integrates PlantTribes scaffold orthogroup backbone |
| 74 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool. | 79 gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool. |