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1 <tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.3">
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2 <description>and inferred maximum likelihood phylogenies</description>
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3 <requirements>
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51
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4 <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis
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5 </requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 <!-- In case the return code has not been set propery check stderr too -->
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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 <command>
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16 <![CDATA[
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17 #import os
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18 #import sys
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19
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20 #set input_format = $input_format_cond.input_format
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21 #set pipeline_output_dir = 'phylogenomicsAnalysis_dir'
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22 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
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23 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
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24 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
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25
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26 #if str($input_format) == 'ptortho':
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27 #set dest_fasta_dir = $output_fasta_ptortho.extra_files_path
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28 #set multiple_codon_alignments = 'no'
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29 #set use_corresponding_coding_sequences = 'no'
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30 #else:
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31 #set dest_fasta_dir = $output_fasta_ptorthocs.extra_files_path
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32 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
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33 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
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34 #if str($multiple_codon_alignments) == 'yes':
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35 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
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36 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
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37 #else:
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38 #set use_corresponding_coding_sequences = 'no'
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39 #end if
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40 #end if
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42
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41 mkdir -p $dest_fasta_dir &&
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42
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43 #if str($options_type.options_type_selector) == 'advanced':
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44 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
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45 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
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46 #if str($multiple_sequence_alignments) == 'yes':
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47 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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48 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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49 #set generate_output_aln = True
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50 #set dest_aln_dir = $output_aln.extra_files_path
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51 mkdir -p $dest_aln_dir &&
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52 #else:
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53 #set generate_output_aln = False
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54 #end if
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48
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55 #else:
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56 #set generate_output_aln = False
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46
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57 #end if
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58
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59 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
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60 #set generate_output_tree = True
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61 #set dest_tree_dir = $output_tree.extra_files_path
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62 mkdir -p $dest_tree_dir &&
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63 #else:
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64 #set generate_output_tree = False
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65 #end if
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66
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67 PhylogenomicsAnalysis
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68 --num_threads \${GALAXY_SLOTS:-4}
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69 #if str($input_format) == 'ptortho':
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70 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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47
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71 #else:
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72 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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73 --orthogroup_fna
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74 #end if
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75 --config_dir '$scaffold.fields.path'
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76 --scaffold '$scaffold.fields.path'
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77 --method $method
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78
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79 #if str($options_type.options_type_selector) == 'advanced':
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80 #if str($multiple_sequence_alignments) == 'yes':
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81 #if str($multiple_sequence_alignments_option) == 'create_alignments':
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82 --create_alignments
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83 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
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84 --add_alignments
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85 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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86 --pasta_script_path '$__tool_directory__/run_pasta.py'
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87 --pasta_alignments
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88 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
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89 #end if
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90 #end if
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91
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92 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
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93 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
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94 #set tree_inference_method = $tree_inference_cond.tree_inference
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95 --tree_inference $tree_inference_method
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96 #if str($tree_inference_method) == 'raxml':
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97 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
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98 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
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99 #if str($rooting_order_file) == 'yes':
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100 --rooting_order '$rooting_order_file_cond.rooting_order'
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101 # No else block needed here because the default rooting_order
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102 # configuration will be used if the --rooting_order flag is missing.
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103 #end if
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104 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
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105 #end if
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106 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
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107 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
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108 #end if
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109
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110 #if str($options_type.msa_quality_control_options_cond.msa_quality_control_options) == 'yes':
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111 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
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112 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
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113 #if str($remove_gappy_sequences_cond) == 'yes':
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114 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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115 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
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116 #if str($trim_type_cond.trim_type) == 'automated_trimming':
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117 --automated_trimming
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118 #else:
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119 --gap_trimming $trim_type_cond.gap_trimming
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120 #end if
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121 #end if
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122 #end if
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123 #end if
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124 >/dev/null
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125
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126 && echo "Sequence alignments and corresponding phylogenies"
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127 #if str($input_format) == 'ptortho':
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128 && echo -e "#Size\tName" > $output_fasta_ptortho
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129 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho
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130 #else:
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131 && echo -e "#Size\tName" > $output_fasta_ptorthocs
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132 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs
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133 #end if
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134 #if len($os.listdir($src_fasta_dir)) > 0:
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135 && mv $src_fasta_dir/* $dest_fasta_dir
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136 #end if
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137
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138 #if $generate_output_aln:
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139 && echo -e "#Size\tName" > $output_aln
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140 #if len($os.listdir($src_aln_dir)) > 0:
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141 ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln
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142 && mv $src_aln_dir/* $dest_aln_dir
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143 #end if
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144 #end if
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145
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146 #if $generate_output_tree:
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147 && echo -e "#Size\tName" > $output_tree
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148 #if len($os.listdir($src_tree_dir)) > 0:
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149 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree
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150 && mv $src_tree_dir/* $dest_tree_dir
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151 #end if
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152 #end if
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153 ]]>
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154 </command>
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155 <inputs>
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156 <conditional name="input_format_cond">
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157 <param name="input_format" type="select" label="Select type of data to sub sample">
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158 <option value="ptortho">Precomputed orthologous gene family clusters</option>
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159 <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
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160 </param>
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161 <when value="ptortho">
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162 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
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163 </when>
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164 <when value="ptorthocs">
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165 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
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166 <conditional name="multiple_codon_alignments_cond">
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167 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
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168 <option value="no" selected="True">No</option>
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169 <option value="yes">Yes</option>
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170 </param>
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171 <when value="no" />
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172 <when value="yes">
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173 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
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174 <option value="protein" selected="true">Amino acid based</option>
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175 <option value="dna">Nucleotide based</option>
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176 </param>
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177 <conditional name="use_corresponding_coding_sequences_cond">
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178 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences?">
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179 <option value="no" selected="true">No</option>
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180 <option value="yes">Yes</option>
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181 </param>
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182 <when value="no" />
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183 <when value="yes" />
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184 </conditional>
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185 </when>
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186 </conditional>
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187 </when>
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188 </conditional>
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189 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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190 <options from_data_table="plant_tribes_scaffolds" />
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191 <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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192 </param>
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193 <param name="method" type="select" label="Protein clustering method">
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194 <option value="gfam" selected="true">GFam</option>
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195 <option value="orthofinder">OrthoFinder</option>
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196 <option value="orthomcl">OrthoMCL</option>
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197 </param>
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198 <conditional name="options_type">
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199 <param name="options_type_selector" type="select" label="Options Configuration">
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200 <option value="basic" selected="true">Basic</option>
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201 <option value="advanced">Advanced</option>
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202 </param>
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203 <when value="basic" />
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204 <when value="advanced">
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205 <conditional name="multiple_sequence_alignments_cond">
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206 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
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207 <option value="no" selected="true">No</option>
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208 <option value="yes">Yes</option>
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209 </param>
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210 <when value="no" />
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211 <when value="yes">
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212 <conditional name="multiple_sequence_alignments_option_cond">
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213 <param name="multiple_sequence_alignments_option" label="Select method for multiple sequence alignments" type="select"
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214 force_select="True">
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215 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
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216 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
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217 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
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218 </param>
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219 <when value="create_alignments" />
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220 <when value="add_alignments" />
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221 <when value="pasta_alignments">
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222 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run" />
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223 </when>
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224 </conditional>
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225 </when>
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226 </conditional>
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227 <conditional name="phylogenetic_trees_cond">
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228 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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229 <option value="no" selected="true">No</option>
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230 <option value="yes">Yes</option>
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231 </param>
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232 <when value="no" />
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233 <when value="yes">
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234 <conditional name="tree_inference_cond">
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235 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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236 <option value="raxml" selected="true">RAxML</option>
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237 <option value="fasttree">FastTree</option>
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238 </param>
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239 <when value="raxml">
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240 <conditional name="rooting_order_file_cond">
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241 <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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242 <option value="no" selected="true">No</option>
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243 <option value="yes">Yes</option>
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244 </param>
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245 <when value="no" />
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246 <when value="yes">
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247 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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248 </when>
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249 </conditional>
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250 <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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251 </when>
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252 <when value="fasttree" />
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253 </conditional>
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254 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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255 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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256 </when>
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257 </conditional>
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258 <conditional name="msa_quality_control_options_cond">
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259 <param name="msa_quality_control_options" type="select" label="Set MSA quality control options?">
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260 <option value="no" selected="true">No</option>
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261 <option value="yes">Yes</option>
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262 </param>
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263 <when value="no" />
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264 <when value="yes">
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265 <conditional name="remove_gappy_sequences_cond">
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266 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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267 <option value="no" selected="true">No</option>
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268 <option value="yes">Yes</option>
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269 </param>
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270 <when value="no" />
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271 <when value="yes">
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272 <param name="remove_sequences" 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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0
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273 <conditional name="trim_type_cond">
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274 <param name="trim_type" type="select" label="Select process used for gap trimming">
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51
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275 <option value="gap_trimming" selected="true">Nucleotide based </option>
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26
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276 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
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0
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277 </param>
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51
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278 <when value="automated_trimming" />
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279 <when value="gap_trimming">
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280 <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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0
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281 </when>
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282 </conditional>
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283 </when>
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284 </conditional>
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285 </when>
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286 </conditional>
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287 </when>
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288 </conditional>
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289 </inputs>
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290 <outputs>
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51
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291 <data name="output_fasta_ptortho" format="ptortho">
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292 <filter>input_format_cond['input_format'] == 'ptortho'</filter>
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41
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293 </data>
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51
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294 <data name="output_fasta_ptorthocs" format="ptorthocs">
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295 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
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41
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296 </data>
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54
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297 <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
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22
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298 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
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14
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299 </data>
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53
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300 <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
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301 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
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302 </data>
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0
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303 </outputs>
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304 <tests>
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305 <test>
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306 </test>
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307 </tests>
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308 <help>
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59
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309 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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310 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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311 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
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312 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
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313
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59
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314 -----
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315
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59
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316 **Options**
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317
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59
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318 * **Required options**
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18
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319
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59
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320 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
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321 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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322 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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323
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324 * **Multiple sequence alignments options**
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14
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325
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59
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326 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
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327 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
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328 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
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329 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
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330 - **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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14
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331
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59
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332 * **Phylogenetic trees options**
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15
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333
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59
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334 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
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335 - **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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336 - **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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337 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
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338 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
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14
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339
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59
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340 * **MSA quality control options**
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14
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341
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59
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342 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
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343 - **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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344 - **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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14
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345
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0
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346 </help>
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347 <citations>
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51
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348 <citation type="bibtex">
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349 @unpublished{None,
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350 author = {Eric Wafula},
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351 title = {None},
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352 year = {None},
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353 url = {https://github.com/dePamphilis/PlantTribes}
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354 }
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355 </citation>
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356 <citation type="doi">10.1093/bioinformatics/btw412</citation>
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357 <citation type="bibtex">
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358 @published{Research in Computational Molecular Biology (RECOMB) (pp. 177–191),
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359 author = {Mirarab, S., Nguyen, N., Warnow, T.},
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360 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan
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361 (Ed.)},
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362 year = {2014},
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363 url = {https://github.com/smirarab/pasta}
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364 }
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365 </citation>
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366 <citation type="bibtex">
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367 @published{Bioinformatics,
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368 author = {Salvador Capella-Gutierrez, Jose M. Silla-Martinez, Toni
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369 Gabaldon},
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370 title = {trimAl: a tool for automated alignment trimming in large-scale
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371 phylogenetic analyses},
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372 year = {2009},
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373 url = {http://trimal.cgenomics.org}
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374 }
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375 </citation>
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376 <citation type="bibtex">
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377 @published{Bioinformatics,
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378 author = {A. Stamatakis},
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379 title = {RAxML Version 8: A tool for Phylogenetic Analysis and
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380 Post-Analysis of Large Phylogenies},
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381 year = {2014},
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382 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html}
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383 }
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384 </citation>
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385 <citation type="doi">10.1371/journal.pone.0009490</citation>
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0
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386 </citations>
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387 </tool>
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