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72
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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">
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4 <requirements>
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5 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="stdio">
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9 <stdio>
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10 <exit_code range="1:"/>
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11 <exit_code range=":-1"/>
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12 <regex match="Error:"/>
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13 <regex match="Exception:"/>
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14 </stdio>
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15 </xml>
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16 <xml name="param_scaffold">
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17 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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18 <options from_data_table="plant_tribes_scaffolds" />
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19 <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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20 </param>
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21 </xml>
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22 <xml name="param_method">
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23 <param name="method" type="select" label="Protein clustering method">
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24 <option value="gfam" selected="true">GFam</option>
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25 <option value="orthofinder">OrthoFinder</option>
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26 <option value="orthomcl">OrthoMCL</option>
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27 </param>
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28 </xml>
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29 <xml name="param_options_type">
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30 <param name="options_type" type="select" label="Options Configuration">
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31 <option value="basic" selected="true">Basic</option>
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32 <option value="advanced">Advanced</option>
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33 </param>
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34 </xml>
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83
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35 <xml name="cond_orthogroup_fna">
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36 <conditional name="orthogroup_fna_cond">
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37 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
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38 <option value="yes" selected="true">Yes</option>
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39 <option value="no">No</option>
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40 </param>
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41 <when value="yes">
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42 <conditional name="options_type_cond">
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85
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43 <expand macro="param_options_type" />
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83
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44 <when value="basic" />
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45 <when value="advanced">
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88
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46 <expand macro="cond_remove_gappy_sequences" />
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83
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47 <expand macro="cond_phylogenetic_trees_ptorthocs" />
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48 <expand macro="param_multiple_codon_alignments" />
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49 </when>
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50 </conditional>
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51 </when>
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52 <when value="no">
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53 <conditional name="options_type_cond">
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86
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54 <expand macro="param_options_type" />
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83
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55 <when value="basic" />
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56 <when value="advanced">
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88
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57 <expand macro="cond_remove_gappy_sequences" />
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83
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58 <expand macro="cond_phylogenetic_trees_ptorthocs" />
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59 </when>
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60 </conditional>
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61 </when>
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62 </conditional>
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81
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63 </xml>
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90
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64 <xml name="param_multiple_sequence_alignments">
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65 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
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66 <option value="no" selected="true">No</option>
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67 <option value="yes">Yes</option>
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68 </param>
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69 </xml>
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94
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70 <xml name="options_multiple_sequence_alignments_option">
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71 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
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72 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
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73 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
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74 </xml>
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90
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75 <xml name="param_multiple_sequence_alignments_option">
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76 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
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94
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77 <expand macro="options_multiple_sequence_alignments_option" />
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90
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78 </param>
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79 </xml>
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91
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80 <xml name="cond_multiple_sequence_alignments_option_with_iterative_realignments">
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81 <conditional name="multiple_sequence_alignments_option_cond">
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82 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
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94
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83 <expand macro="options_multiple_sequence_alignments_option" />
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91
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84 <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option>
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85 </param>
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86 <expand macro="whens_multiple_sequence_alignments_option_cond" />
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87 <when value="iterative_realignments">
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88 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
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89 </when>
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90 </conditional>
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91 </xml>
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90
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92 <xml name="whens_multiple_sequence_alignments_option_cond">
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93 <when value="create_alignments" />
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94 <when value="add_alignments" />
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95 <when value="pasta_alignments">
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96 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
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97 </when>
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98 </xml>
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72
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99 <xml name="cond_multiple_sequence_alignments">
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100 <conditional name="multiple_sequence_alignments_cond">
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90
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101 <expand macro="param_multiple_sequence_alignments" />
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72
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102 <when value="no" />
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103 <when value="yes">
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104 <conditional name="multiple_sequence_alignments_option_cond">
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93
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105 <expand macro="param_multiple_sequence_alignments_option" />
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90
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106 <expand macro="whens_multiple_sequence_alignments_option_cond" />
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72
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107 </conditional>
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108 </when>
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109 </conditional>
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110 </xml>
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91
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111 <xml name="cond_multiple_sequence_alignments_with_iterative_realignments">
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112 <conditional name="multiple_sequence_alignments_cond">
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113 <expand macro="param_multiple_sequence_alignments" />
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114 <when value="no" />
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115 <when value="yes">
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116 <conditional name="multiple_sequence_alignments_option_cond">
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93
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117 <expand macro="param_multiple_sequence_alignments_option" />
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91
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118 <expand macro="whens_multiple_sequence_alignments_option_cond" />
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92
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119 <expand macro="cond_multiple_sequence_alignments_option_with_iterative_realignments" />
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91
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120 </conditional>
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121 </when>
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122 </conditional>
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123 </xml>
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79
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124 <xml name="cond_phylogenetic_trees_ptortho">
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72
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125 <conditional name="phylogenetic_trees_cond">
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126 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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127 <option value="no" selected="true">No</option>
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128 <option value="yes">Yes</option>
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129 </param>
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130 <when value="no" />
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131 <when value="yes">
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132 <conditional name="tree_inference_cond">
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133 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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134 <option value="raxml" selected="true">RAxML</option>
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135 <option value="fasttree">FastTree</option>
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136 </param>
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137 <when value="raxml">
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138 <conditional name="rooting_order_file_cond">
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139 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
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140 <option value="no" selected="true">No</option>
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141 <option value="yes">Yes</option>
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142 </param>
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143 <when value="no" />
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144 <when value="yes">
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145 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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146 </when>
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147 </conditional>
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148 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
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149 </when>
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150 <when value="fasttree" />
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151 </conditional>
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152 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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153 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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75
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154 </when>
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155 </conditional>
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74
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156 </xml>
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79
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157 <xml name="cond_phylogenetic_trees_ptorthocs">
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75
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158 <conditional name="phylogenetic_trees_cond">
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159 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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160 <option value="no" selected="true">No</option>
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161 <option value="yes">Yes</option>
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162 </param>
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163 <when value="no" />
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164 <when value="yes">
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165 <conditional name="tree_inference_cond">
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166 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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167 <option value="raxml" selected="true">RAxML</option>
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168 <option value="fasttree">FastTree</option>
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169 </param>
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170 <when value="raxml">
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171 <conditional name="rooting_order_file_cond">
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172 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
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173 <option value="no" selected="true">No</option>
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174 <option value="yes">Yes</option>
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175 </param>
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176 <when value="no" />
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177 <when value="yes">
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178 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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179 </when>
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180 </conditional>
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181 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
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182 </when>
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183 <when value="fasttree" />
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184 </conditional>
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185 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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186 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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187 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
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188 <option value="protein" selected="true">Amino acid based</option>
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189 <option value="dna">Nucleotide based</option>
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190 </param>
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72
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191 </when>
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192 </conditional>
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193 </xml>
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194 <xml name="cond_remove_gappy_sequences">
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195 <conditional name="remove_gappy_sequences_cond">
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196 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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197 <option value="no" selected="true">No</option>
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198 <option value="yes">Yes</option>
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199 </param>
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88
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200 <when value="no">
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201 <expand macro="cond_multiple_sequence_alignments" />
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202 </when>
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72
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203 <when value="yes">
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204 <conditional name="trim_type_cond">
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205 <param name="trim_type" type="select" label="Select process used for gap trimming">
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206 <option value="gap_trimming" selected="true">Nucleotide based </option>
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207 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
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208 </param>
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209 <when value="automated_trimming" />
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210 <when value="gap_trimming">
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211 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
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212 </when>
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213 </conditional>
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214 <conditional name="remove_sequences_with_gaps_cond">
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215 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
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216 <option value="no" selected="true">No</option>
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217 <option value="yes">Yes</option>
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218 </param>
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91
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219 <when value="no">
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220 <expand macro="cond_multiple_sequence_alignments" />
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221 </when>
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72
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222 <when value="yes">
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223 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
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91
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224 <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" />
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72
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225 </when>
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226 </conditional>
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227 </when>
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228 </conditional>
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229 </xml>
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74
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230 <xml name="param_multiple_codon_alignments">
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231 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
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232 <option value="no" selected="True">No</option>
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233 <option value="yes">Yes</option>
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234 </param>
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72
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235 </xml>
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236 <xml name="citations">
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237 <citations>
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238 <citation type="bibtex">
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239 @misc{None,
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240 journal = {None},
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241 author = {1. Wafula EK},
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242 title = {Manuscript in preparation},
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243 year = {None},
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244 url = {https://github.com/dePamphilis/PlantTribes},}
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245 </citation>
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246 <citation type="bibtex">
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247 @article{Mirarab2014,
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248 journal = {Research in Computational Molecular Biology (RECOMB)},
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249 author = {2. Mirarab S, Nguyen N, Warnow T},
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250 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
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251 year = {2014},
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252 pages = {177–191},
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253 url = {https://github.com/smirarab/pasta},}
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254 </citation>
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255 <citation type="bibtex">
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256 @article{Salvador2009,
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257 journal = {Bioinformatics},
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258 author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
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259 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
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260 year = {2009},
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261 url = {http://trimal.cgenomics.org},}
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262 </citation>
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263 <citation type="bibtex">
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264 @article{Stamatakis2014,
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265 journal = {Bioinformatics},
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266 author = {4. Stamatakis A},
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267 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
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268 year = {2014},
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269 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
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270 </citation>
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271 <citation type="doi">10.1371/journal.pone.0009490</citation>
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272 <citation type="doi">10.1093/bioinformatics/btw412</citation>
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273 </citations>
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274 </xml>
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275 </macros>
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