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