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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3 <xml name="requirements_assembly_post_processor">
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4 <requirements>
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5 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="requirements_gene_family_classifier">
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9 <requirements>
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10 <requirement type="package" version="0.4">plant_tribes_gene_family_classifier</requirement>
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11 </requirements>
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12 </xml>
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13 <xml name="requirements_gene_family_integrator">
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14 <requirements>
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15 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
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16 </requirements>
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17 </xml>
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18 <xml name="stdio">
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19 <stdio>
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20 <exit_code range="1:"/>
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21 <exit_code range=":-1"/>
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22 <regex match="Error:"/>
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23 <regex match="Exception:"/>
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24 </stdio>
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25 </xml>
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26 <xml name="param_scaffold">
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27 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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28 <options from_data_table="plant_tribes_scaffolds" />
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29 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
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30 </param>
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31 </xml>
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32 <xml name="param_method">
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33 <param name="method" type="select" label="Protein clustering method">
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34 <option value="gfam" selected="true">GFam</option>
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35 <option value="orthofinder">OrthoFinder</option>
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36 <option value="orthomcl">OrthoMCL</option>
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37 </param>
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38 </xml>
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39 <xml name="param_orthogroup_fna">
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40 <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
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41 <option value="yes" selected="true">Yes</option>
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42 <option value="no">No</option>
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43 </param>
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44 </xml>
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45 <xml name="citation1">
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46 <citation type="bibtex">
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47 @misc{None,
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48 journal = {None},
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49 author = {1. Wafula EK},
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50 title = {Manuscript in preparation},
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51 year = {None},
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52 url = {https://github.com/dePamphilis/PlantTribes},}
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53 </citation>
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54 </xml>
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55 <xml name="citations2to4">
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56 <citation type="bibtex">
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57 @article{Sasidharan2012,
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58 journal = {Nucleic Acids Research},
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59 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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60 title = {GFam: a platform for automatic annotation of gene families},
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61 year = {2012},
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62 pages = {gks631},}
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63 </citation>
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64 <citation type="bibtex">
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65 @article{Li2003,
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66 journal = {Genome Research}
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67 author = {3. Li L, Stoeckert CJ, Roos DS},
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68 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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69 year = {2003},
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70 volume = {13},
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71 number = {9},
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72 pages = {2178-2189},}
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73 </citation>
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74 <citation type="bibtex">
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75 @article{Emms2015,
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76 journal = {Genome Biology}
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77 author = {4. Emms DM, Kelly S},
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78 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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79 year = {2015},
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80 volume = {16},
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81 number = {1},
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82 pages = {157},}
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83 </citation>
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84 </xml>
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85 </macros>
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