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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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99
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16 <token name="@REMOVE_GAPPY_SEQUENCES_COND_PREP@">
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98
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17 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
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18 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
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19 #if str($remove_gappy_sequences) == 'no':
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20 #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond
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21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
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22 #if str($multiple_sequence_alignments) == 'yes':
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23 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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24 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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25 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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26 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
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27 #end if
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28 #end if
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29 #else:
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30 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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31 #set trim_type = $trim_type_cond.trim_type
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32 #if str($trim_type) == 'gap_trimming':
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33 #set gap_trimming = $trim_type_cond.gap_trimming
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34 #end if
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35 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
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36 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
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37 #if str($remove_sequences_with_gaps) == 'no':
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38 #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond
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39 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
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40 #if str($multiple_sequence_alignments) == 'yes':
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41 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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42 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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43 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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44 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
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45 #end if
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46 #end if
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47 #else:
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48 #set remove_sequences_with_gaps_of = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
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49 #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond
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50 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
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51 #if str($multiple_sequence_alignments) == 'yes':
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52 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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53 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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54 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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55 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit
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99
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56 #else if str($multiple_sequence_alignments_option) == 'iterative_realignment':
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57 #set iterative_realignment = $multiple_sequence_alignments_option_cond.iterative_realignment
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98
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58 #end if
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59 #end if
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60 #end if
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61 #end if
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62 </token>
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99
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63 <token name="@REMOVE_GAPPY_SEQUENCES_COND_CMD@">
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64 #if str($remove_gappy_sequences) == 'no':
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65 #if str($multiple_sequence_alignments) == 'yes':
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66 --alignments_method $multiple_sequence_alignments_option
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67 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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68 --pasta_script_path '$__tool_directory__/run_pasta.py'
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69 --pasta_iter_limit $pasta_iter_limit
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70 #end if
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71 #end if
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72 #else:
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73 ## str($remove_gappy_sequences) == 'yes':
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74 --trim_type $trim_type
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75 #if str($trim_type) == 'gap_trimming':
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76 --gap_trimming $gap_trimming
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77 #end if
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78 #if str($remove_sequences_with_gaps) == 'no':
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79 #if str($multiple_sequence_alignments) == 'yes':
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80 --alignments_method $multiple_sequence_alignments_option
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81 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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82 --pasta_script_path '$__tool_directory__/run_pasta.py'
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83 --pasta_iter_limit $pasta_iter_limit
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84 #end if
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85 #end if
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86 #else:
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87 ## str($remove_sequences_with_gaps) == 'yes':
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88 --remove_sequences $remove_sequences_with_gaps_of
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89 #if str($multiple_sequence_alignments) == 'yes':
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90 --alignments_method $multiple_sequence_alignments_option
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91 #if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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92 --pasta_script_path '$__tool_directory__/run_pasta.py'
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93 --pasta_iter_limit $pasta_iter_limit
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94 #else:
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95 --iterative_realignment $iterative_realignment
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96 #end if
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97 #end if
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98 #end if
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99 #end if
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100 </token>
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101 <token name="@SET_PHYLOGENETIC_TREES_PREP@">
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98
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102 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
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103 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
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104 </token>
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99
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105 <token name="@TREE_INFERENCE_COND_PREP@">
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98
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106 #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
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107 #set tree_inference = $tree_inference_cond.tree_inference
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108 #if str($tree_inference) == 'raxml':
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109 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
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110 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
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111 #if str($rooting_order_file) == 'yes':
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112 #set rooting_order = $rooting_order_file_cond.rooting_order
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113 #end if
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114 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
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115 #end if
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99
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116 #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size
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98
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117 #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size
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99
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118 </token>
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119 <token name="@TREE_INFERENCE_COND_CMD@">
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120 --tree_inference $tree_inference
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121 #if str($tree_inference) == 'raxml':
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122 #if str($rooting_order_file) == 'yes':
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123 --rooting_order '$rooting_order'
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124 ## No else block needed here because the default rooting_order
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125 ## configuration will be used if the --rooting_order flag is missing.
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126 #end if
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127 --bootstrap_replicates $bootstrap_replicates
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128 #end if
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129 --min_orthogroup_size $min_orthogroup_size
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130 --max_orthogroup_size $max_orthogroup_size
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98
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131 </token>
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105
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132 <token name="@OUTPUT_ALN@">
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107
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133 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and ((str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences']) == 'yes' and str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes') or (str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes') and str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes')):
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105
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134 --output_aln '$output_aln'
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135 --output_aln_dir '$output_aln.files_path'
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136 #end if
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137 </token>
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138 <token name="@OUTPUT_TREE@">
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139 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and str($input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees']) == 'yes':
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140 --output_tree '$output_tree'
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141 --output_tree_dir '$output_tree.files_path'
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142 #end if
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143 </token>
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72
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144 <xml name="param_scaffold">
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145 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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146 <options from_data_table="plant_tribes_scaffolds" />
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147 <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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148 </param>
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149 </xml>
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150 <xml name="param_method">
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151 <param name="method" type="select" label="Protein clustering method">
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152 <option value="gfam" selected="true">GFam</option>
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153 <option value="orthofinder">OrthoFinder</option>
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154 <option value="orthomcl">OrthoMCL</option>
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155 </param>
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156 </xml>
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157 <xml name="param_options_type">
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158 <param name="options_type" type="select" label="Options Configuration">
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159 <option value="basic" selected="true">Basic</option>
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160 <option value="advanced">Advanced</option>
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161 </param>
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162 </xml>
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83
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163 <xml name="cond_orthogroup_fna">
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164 <conditional name="orthogroup_fna_cond">
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165 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
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166 <option value="yes" selected="true">Yes</option>
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167 <option value="no">No</option>
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168 </param>
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169 <when value="yes">
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170 <conditional name="options_type_cond">
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85
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171 <expand macro="param_options_type" />
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83
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172 <when value="basic" />
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173 <when value="advanced">
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88
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174 <expand macro="cond_remove_gappy_sequences" />
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97
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175 <expand macro="param_multiple_codon_alignments" />
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83
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176 <expand macro="cond_phylogenetic_trees_ptorthocs" />
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177 </when>
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178 </conditional>
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179 </when>
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180 <when value="no">
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181 <conditional name="options_type_cond">
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86
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182 <expand macro="param_options_type" />
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83
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183 <when value="basic" />
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184 <when value="advanced">
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88
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185 <expand macro="cond_remove_gappy_sequences" />
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83
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186 <expand macro="cond_phylogenetic_trees_ptorthocs" />
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187 </when>
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188 </conditional>
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189 </when>
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190 </conditional>
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81
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191 </xml>
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90
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192 <xml name="param_multiple_sequence_alignments">
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193 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
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194 <option value="no" selected="true">No</option>
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195 <option value="yes">Yes</option>
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196 </param>
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197 </xml>
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94
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198 <xml name="options_multiple_sequence_alignments_option">
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199 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
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200 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
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201 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
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202 </xml>
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90
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203 <xml name="param_multiple_sequence_alignments_option">
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204 <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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205 <expand macro="options_multiple_sequence_alignments_option" />
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90
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206 </param>
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207 </xml>
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99
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208 <xml name="param_multiple_sequence_alignments_option_with_iterative_realignment">
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96
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209 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
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210 <expand macro="options_multiple_sequence_alignments_option" />
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99
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211 <option value="iterative_realignment">Iterative orthogroups realignment, trimming and fitering</option>
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96
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212 </param>
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91
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213 </xml>
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90
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214 <xml name="whens_multiple_sequence_alignments_option_cond">
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215 <when value="create_alignments" />
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216 <when value="add_alignments" />
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217 <when value="pasta_alignments">
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218 <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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219 </when>
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220 </xml>
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72
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221 <xml name="cond_multiple_sequence_alignments">
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222 <conditional name="multiple_sequence_alignments_cond">
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90
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223 <expand macro="param_multiple_sequence_alignments" />
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72
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224 <when value="no" />
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225 <when value="yes">
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226 <conditional name="multiple_sequence_alignments_option_cond">
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93
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227 <expand macro="param_multiple_sequence_alignments_option" />
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90
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228 <expand macro="whens_multiple_sequence_alignments_option_cond" />
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72
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229 </conditional>
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230 </when>
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231 </conditional>
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232 </xml>
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99
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233 <xml name="cond_multiple_sequence_alignments_with_iterative_realignment">
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91
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234 <conditional name="multiple_sequence_alignments_cond">
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235 <expand macro="param_multiple_sequence_alignments" />
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236 <when value="no" />
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237 <when value="yes">
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238 <conditional name="multiple_sequence_alignments_option_cond">
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99
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239 <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignment" />
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91
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240 <expand macro="whens_multiple_sequence_alignments_option_cond" />
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99
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241 <when value="iterative_realignment">
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242 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
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96
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243 </when>
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91
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244 </conditional>
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245 </when>
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246 </conditional>
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247 </xml>
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79
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248 <xml name="cond_phylogenetic_trees_ptortho">
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72
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249 <conditional name="phylogenetic_trees_cond">
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250 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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251 <option value="no" selected="true">No</option>
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252 <option value="yes">Yes</option>
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253 </param>
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254 <when value="no" />
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255 <when value="yes">
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256 <conditional name="tree_inference_cond">
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257 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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258 <option value="raxml" selected="true">RAxML</option>
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259 <option value="fasttree">FastTree</option>
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260 </param>
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261 <when value="raxml">
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262 <conditional name="rooting_order_file_cond">
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263 <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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264 <option value="no" selected="true">No</option>
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265 <option value="yes">Yes</option>
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266 </param>
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267 <when value="no" />
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268 <when value="yes">
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269 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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270 </when>
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271 </conditional>
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272 <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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273 </when>
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274 <when value="fasttree" />
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275 </conditional>
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276 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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277 <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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278 </when>
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279 </conditional>
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74
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280 </xml>
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79
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281 <xml name="cond_phylogenetic_trees_ptorthocs">
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75
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282 <conditional name="phylogenetic_trees_cond">
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283 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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284 <option value="no" selected="true">No</option>
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285 <option value="yes">Yes</option>
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286 </param>
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287 <when value="no" />
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288 <when value="yes">
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289 <conditional name="tree_inference_cond">
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290 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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291 <option value="raxml" selected="true">RAxML</option>
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292 <option value="fasttree">FastTree</option>
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293 </param>
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294 <when value="raxml">
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295 <conditional name="rooting_order_file_cond">
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296 <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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297 <option value="no" selected="true">No</option>
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298 <option value="yes">Yes</option>
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299 </param>
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300 <when value="no" />
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301 <when value="yes">
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302 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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303 </when>
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304 </conditional>
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305 <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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306 </when>
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307 <when value="fasttree" />
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308 </conditional>
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309 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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310 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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311 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
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312 <option value="protein" selected="true">Amino acid based</option>
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313 <option value="dna">Nucleotide based</option>
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314 </param>
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72
|
315 </when>
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316 </conditional>
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317 </xml>
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318 <xml name="cond_remove_gappy_sequences">
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319 <conditional name="remove_gappy_sequences_cond">
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320 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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|
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321 <option value="no" selected="true">No</option>
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322 <option value="yes">Yes</option>
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|
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323 </param>
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88
|
324 <when value="no">
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325 <expand macro="cond_multiple_sequence_alignments" />
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326 </when>
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72
|
327 <when value="yes">
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328 <conditional name="trim_type_cond">
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329 <param name="trim_type" type="select" label="Select process used for gap trimming">
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330 <option value="gap_trimming" selected="true">Nucleotide based </option>
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331 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
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|
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332 </param>
|
|
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333 <when value="gap_trimming">
|
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106
|
334 <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
|
|
72
|
335 </when>
|
|
98
|
336 <when value="automated_trimming" />
|
|
72
|
337 </conditional>
|
|
|
338 <conditional name="remove_sequences_with_gaps_cond">
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339 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
|
|
|
340 <option value="no" selected="true">No</option>
|
|
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341 <option value="yes">Yes</option>
|
|
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342 </param>
|
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91
|
343 <when value="no">
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|
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344 <expand macro="cond_multiple_sequence_alignments" />
|
|
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345 </when>
|
|
72
|
346 <when value="yes">
|
|
106
|
347 <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
|
|
99
|
348 <expand macro="cond_multiple_sequence_alignments_with_iterative_realignment" />
|
|
72
|
349 </when>
|
|
|
350 </conditional>
|
|
|
351 </when>
|
|
|
352 </conditional>
|
|
|
353 </xml>
|
|
74
|
354 <xml name="param_multiple_codon_alignments">
|
|
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355 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
|
|
|
356 <option value="no" selected="True">No</option>
|
|
|
357 <option value="yes">Yes</option>
|
|
|
358 </param>
|
|
72
|
359 </xml>
|
|
100
|
360 <xml name="output_ptortho">
|
|
|
361 <data name="output_ptortho" format="ptortho">
|
|
|
362 <filter>input_format_cond['input_format'] == 'ptortho'</filter>
|
|
|
363 </data>
|
|
|
364 </xml>
|
|
|
365 <xml name="output_ptorthocs">
|
|
|
366 <data name="output_ptorthocs" format="ptorthocs">
|
|
|
367 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
|
|
|
368 </data>
|
|
|
369 </xml>
|
|
|
370 <xml name="output_aln">
|
|
|
371 <data name="output_aln" format="ptalign" label="${tool.name} on ${on_string} (multiple alignments)">
|
|
101
|
372 <filter>input_format_cond['options_type_cond']['options_type'] == 'advanced' and ((input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes') or (input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes' and input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'))</filter>
|
|
100
|
373 </data>
|
|
|
374 </xml>
|
|
|
375 <xml name="output_tree">
|
|
|
376 <data name="output_tree" format="pttree" label="${tool.name} on ${on_string} (phylogenetic trees)">
|
|
|
377 <filter>input_format_cond['options_type_cond']['options_type'] == 'advanced' and input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
|
|
|
378 </data>
|
|
|
379 </xml>
|
|
72
|
380 <xml name="citations">
|
|
|
381 <citations>
|
|
|
382 <citation type="bibtex">
|
|
|
383 @misc{None,
|
|
|
384 journal = {None},
|
|
|
385 author = {1. Wafula EK},
|
|
|
386 title = {Manuscript in preparation},
|
|
|
387 year = {None},
|
|
|
388 url = {https://github.com/dePamphilis/PlantTribes},}
|
|
|
389 </citation>
|
|
|
390 <citation type="bibtex">
|
|
|
391 @article{Mirarab2014,
|
|
|
392 journal = {Research in Computational Molecular Biology (RECOMB)},
|
|
|
393 author = {2. Mirarab S, Nguyen N, Warnow T},
|
|
|
394 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
|
|
|
395 year = {2014},
|
|
|
396 pages = {177–191},
|
|
|
397 url = {https://github.com/smirarab/pasta},}
|
|
|
398 </citation>
|
|
|
399 <citation type="bibtex">
|
|
|
400 @article{Salvador2009,
|
|
|
401 journal = {Bioinformatics},
|
|
|
402 author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
|
|
|
403 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
|
|
|
404 year = {2009},
|
|
|
405 url = {http://trimal.cgenomics.org},}
|
|
|
406 </citation>
|
|
|
407 <citation type="bibtex">
|
|
|
408 @article{Stamatakis2014,
|
|
|
409 journal = {Bioinformatics},
|
|
|
410 author = {4. Stamatakis A},
|
|
|
411 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
|
|
|
412 year = {2014},
|
|
|
413 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
|
|
|
414 </citation>
|
|
|
415 <citation type="doi">10.1371/journal.pone.0009490</citation>
|
|
|
416 <citation type="doi">10.1093/bioinformatics/btw412</citation>
|
|
|
417 </citations>
|
|
|
418 </xml>
|
|
|
419 </macros>
|
