Mercurial > repos > greg > gene_family_integrator
comparison gene_family_integrator.xml @ 0:109a0eb7791f draft
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| author | greg |
|---|---|
| date | Thu, 06 Apr 2017 13:34:02 -0400 |
| parents | |
| children | bbc56c8688ff |
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| -1:000000000000 | 0:109a0eb7791f |
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| 1 <tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="0.8.0"> | |
| 2 <description>integrates de novo assembly sequences with scaffold gene family sequences</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements_gene_family_integrator" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 #set input_format = $input_format_cond.input_format | |
| 11 #set scaffold = $input_format_cond.scaffold | |
| 12 #set method = $input_format_cond.method | |
| 13 | |
| 14 python $__tool_directory__/gene_family_integrator.py | |
| 15 --scaffold '$scaffold.fields.path' | |
| 16 --method $method | |
| 17 #if str($input_format) == 'ptortho': | |
| 18 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' | |
| 19 #else: | |
| 20 ## str($input_format) == 'ptorthocs' | |
| 21 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' | |
| 22 #if str($orthogroup_fna) == 'yes': | |
| 23 --orthogroup_fna 'true' | |
| 24 #end if | |
| 25 #end if | |
| 26 --output '$output_html' | |
| 27 --output_dir '$output_html.files_path' | |
| 28 ]]> | |
| 29 </command> | |
| 30 <inputs> | |
| 31 <conditional name="input_format_cond"> | |
| 32 <param name="input_format" type="select" label="Select type of data to sub sample"> | |
| 33 <option value="ptortho">Gene family clusters</option> | |
| 34 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option> | |
| 35 </param> | |
| 36 <when value="ptortho"> | |
| 37 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" /> | |
| 38 <expand macro="param_scaffold" /> | |
| 39 <expand macro="param_method" /> | |
| 40 </when> | |
| 41 <when value="ptorthocs"> | |
| 42 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" /> | |
| 43 <expand macro="param_scaffold" /> | |
| 44 <expand macro="param_method" /> | |
| 45 <expand macro="param_orthogroup_fna" /> | |
| 46 </when> | |
| 47 </conditional> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data name="output_html" format="html" /> | |
| 51 </outputs> | |
| 52 <tests> | |
| 53 <test> | |
| 54 </test> | |
| 55 </tests> | |
| 56 <help> | |
| 57 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary | |
| 58 analyses of genome-scale gene families and transcriptomes. This tool integrates classified post processed de novo transcriptome | |
| 59 assembly sequence(s) with the scaffold gene family sequences. | |
| 60 | |
| 61 ----- | |
| 62 | |
| 63 **Required options** | |
| 64 | |
| 65 * **Gene family clusters** - sequences classified into gene family clusters, optionally including corresponding coding sequences. | |
| 66 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool. | |
| 67 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. | |
| 68 | |
| 69 **Other options** | |
| 70 | |
| 71 * Process corresponding gene family classification orthogroups CDS fasta files? - Select 'Yes' top process corresponding gene family classification orthogroups CDS fasta files. | |
| 72 | |
| 73 </help> | |
| 74 <citations> | |
| 75 <expand macro="citation1" /> | |
| 76 <expand macro="citations2to4" /> | |
| 77 </citations> | |
| 78 </tool> |