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1 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="0.6.0">
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2 <description>builds gene family multiple sequence alignments and their corresponding phylogenies</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" />
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7 <expand macro="stdio" />
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0
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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 = $input_format_cond.method
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98
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13
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14 #if str($input_format) == 'ptortho':
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15 #set options_type_cond = $input_format_cond.options_type_cond
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16 #else:
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17 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
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18 #set orthogroup_fna= $orthogroup_fna_cond.orthogroup_fna
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19 #set options_type_cond = $orthogroup_fna_cond.options_type_cond
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20 #endif
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21 #set options_type= $options_type_cond.options_type
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22
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23 #if str($options_type) == 'advanced':
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24 #if str($input_format) == 'ptortho':
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25 @REMOVE_GAPPY_SEQUENCES_COND@
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26 @SET_PHYLOGENETIC_TREES@
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27 #if str($phylogenetic_trees) == 'yes':
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28 @TREE_INFERENCE_COND@
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29 #set sequence_type = 'protein'
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30 #end if
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82
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31 #else:
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32 ## str($input_format) == 'ptorthocs'
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33 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
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34 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna
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35 #set options_type_cond = orthogroup_fna_cond.options_type_cond
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36 #set options_type = $options_type_cond.options_type
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37 #if str($orthogroup_fna) == 'yes':
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38 #if str(options_type) == 'advanced':
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39 @REMOVE_GAPPY_SEQUENCES_COND@
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40 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
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41 @SET_PHYLOGENETIC_TREES@
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42 #if str($phylogenetic_trees) == 'yes':
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43 @TREE_INFERENCE_COND@
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44 #set sequence_type = $phylogenetic_trees_cond.sequence_type
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45 #end if
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46 #end if
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47 #else:
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48 #if str(options_type) == 'advanced':
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49 @REMOVE_GAPPY_SEQUENCES_COND@
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50 @SET_PHYLOGENETIC_TREES@
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51 #if str($phylogenetic_trees) == 'yes':
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52 @TREE_INFERENCE_COND@
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53 #set sequence_type = $phylogenetic_trees_cond.sequence_type
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54 #end if
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55 #end if
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56 #end if
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57 #end if
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14
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58 #end if
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59
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60 python $__tool_directory__/phylogenomics_analysis.py
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61 --num_threads \${GALAXY_SLOTS:-4}
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62 #if str($input_format) == 'ptortho':
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63 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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47
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64 #else:
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65 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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66 #if str($orthogroup_fna) == 'yes':
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67 --orthogroup_fna 'true'
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68 #end if
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69 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
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67
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70 #if str($multiple_codon_alignments) == 'yes':
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71 --codon_alignments 'true'
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67
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72 #end if
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73 #end if
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74 --config_dir '$scaffold.fields.path'
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75 --scaffold '$scaffold.fields.path'
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76 --method $method
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77
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78 #if str($options_type) == 'advanced':
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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 $multiple_sequence_alignments_option_cond.pasta_iter_limit
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84 #end if
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85 #end if
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86
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87 #if str($phylogenetic_trees) == 'yes':
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88 --tree_inference $tree_inference
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89 #if str($tree_inference) == 'raxml':
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90 #if str($rooting_order_file) == 'yes':
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91 --rooting_order '$rooting_order_file_cond.rooting_order'
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92 # No else block needed here because the default rooting_order
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93 # configuration will be used if the --rooting_order flag is missing.
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94 #end if
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95 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
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96 #end if
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97 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
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98 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
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99 --sequence_type $sequence_type
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100 #end if
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101
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102 #if str($remove_gappy_sequences) == 'yes':
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103 #if str($remove_sequences_with_gaps) == 'yes':
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104 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
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105 #end if
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106 --trim_type $trim_type_cond.trim_type
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107 #if str($trim_type_cond.trim_type) == 'gap_trimming':
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108 --gap_trimming $trim_type_cond.gap_trimming
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0
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109 #end if
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110 #end if
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111 #end if
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112
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113 #if str($input_format) == 'ptortho':
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114 --output_ptortho '$output_ptortho'
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115 --output_ptortho_dir '$output_ptortho.files_path'
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42
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116 #else:
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117 --output_ptorthocs '$output_ptorthocs'
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118 --output_ptorthocs_dir '$output_ptorthocs.files_path'
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42
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119 #end if
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120
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121 #if str($multiple_sequence_alignments) == 'yes'
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122 --output_aln '$output_aln'
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123 --output_aln_dir '$output_aln.files_path'
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124 #end if
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125
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126 #if str($phylogenetic_trees) == 'yes':
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127 --output_tree '$output_tree'
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128 --output_tree_dir '$output_tree.files_path'
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129 #end if
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0
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130 ]]>
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131 </command>
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132 <inputs>
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42
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133 <conditional name="input_format_cond">
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134 <param name="input_format" type="select" label="Select type of data to sub sample">
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135 <option value="ptortho">Precomputed orthologous gene family clusters</option>
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136 <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
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137 </param>
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138 <when value="ptortho">
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139 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
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140 <expand macro="param_scaffold" />
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141 <expand macro="param_method" />
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142 <conditional name="options_type_cond">
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143 <expand macro="param_options_type" />
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144 <when value="basic" />
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145 <when value="advanced">
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146 <expand macro="cond_remove_gappy_sequences" />
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147 <expand macro="cond_phylogenetic_trees_ptortho" />
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148 </when>
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149 </conditional>
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150 </when>
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151 <when value="ptorthocs">
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152 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
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153 <expand macro="param_scaffold" />
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154 <expand macro="param_method" />
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155 <expand macro="cond_orthogroup_fna" />
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156 </when>
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157 </conditional>
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158 </inputs>
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159 <outputs>
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160 <data name="output_ptortho" format="ptortho">
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161 <filter>input_format_cond['input_format'] == 'ptortho'</filter>
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162 </data>
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163 <data name="output_ptorthocs" format="ptorthocs">
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164 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
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165 </data>
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166 <data name="output_aln" format="ptalign" label="Multiple alignments (method ${options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']}) on ${on_string}">
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167 <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
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168 </data>
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169 <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
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170 <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
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171 </data>
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172 </outputs>
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173 <tests>
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174 <test>
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175 </test>
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176 </tests>
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177 <help>
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178 This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of
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179 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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180 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
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181 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
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182
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183 -----
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184
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185 **Options**
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186
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187 * **Required**
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188
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189 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
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190 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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191 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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192
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193 * **Multiple sequence alignments**
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194
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195 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
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196 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
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197 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
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198 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
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199 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
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200
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201 * **Phylogenetic trees**
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202
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203 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
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204 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
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205 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
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206 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
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207 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
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208
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209 * **MSA quality control**
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210
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211 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
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212 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
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213 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
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214
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215 </help>
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216 <expand macro="citations" />
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217 </tool>
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