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1 <tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="0.8.0">
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2 <description>integrates de novo assembly sequences with scaffold gene family sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_gene_family_integrator" />
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7 <expand macro="stdio" />
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8 <command>
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9 <![CDATA[
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10 #set input_format = $input_format_cond.input_format
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11 #set scaffold = $input_format_cond.scaffold
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12 #set method = $input_format_cond.method
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13
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14 python $__tool_directory__/gene_family_integrator.py
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15 --scaffold '$scaffold.fields.path'
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16 --method $method
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17 #if str($input_format) == 'ptortho':
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18 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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19 --output '$output_ptortho'
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20 --output_dir '$output_ptortho.files_path'
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21 #else:
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22 ## str($input_format) == 'ptorthocs'
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23 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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4
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24 #if str($input_format_cond.orthogroup_fna) == 'yes':
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25 --orthogroup_fna 'true'
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26 --output '$output_ptorthocs'
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27 --output_dir '$output_ptorthocs.files_path'
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28 #else:
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29 --output '$output_ptortho'
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30 --output_dir '$output_ptortho.files_path'
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31 #end if
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32 #end if
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33 ]]>
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34 </command>
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35 <inputs>
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36 <conditional name="input_format_cond">
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37 <param name="input_format" type="select" label="Select type of data to sub sample">
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38 <option value="ptortho">Gene family clusters</option>
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39 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
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40 </param>
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41 <when value="ptortho">
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42 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" />
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43 <expand macro="param_scaffold" />
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44 <expand macro="param_method" />
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45 </when>
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46 <when value="ptorthocs">
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47 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
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48 <expand macro="param_scaffold" />
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49 <expand macro="param_method" />
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50 <expand macro="param_orthogroup_fna" />
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
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55 <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}">
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56 <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
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57 </data>
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58 <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}">
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59 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test>
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64 </test>
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65 </tests>
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66 <help>
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67 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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68 analyses of genome-scale gene families and transcriptomes. This tool integrates classified post processed de novo transcriptome
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69 assembly sequence(s) with the scaffold gene family sequences.
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70
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71 -----
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72
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73 **Required options**
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74
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75 * **Gene family clusters** - sequences classified into gene family clusters, optionally including corresponding coding sequences.
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76 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
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77 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
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78
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79 **Other options**
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80
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2
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81 * **Process corresponding gene family classification orthogroups CDS fasta files** - Select 'Yes' top process corresponding gene family classification orthogroups CDS fasta files.
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82
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83 </help>
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84 <citations>
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85 <expand macro="citation1" />
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86 <expand macro="citations2to4" />
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87 </citations>
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88 </tool>
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