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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 = $input_format_cond.method
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98
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13
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14 #if str($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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103
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20 #end if
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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($input_format) == 'ptortho':
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25 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
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26 @SET_PHYLOGENETIC_TREES_PREP@
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27 #if str($phylogenetic_trees) == 'yes':
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28 @TREE_INFERENCE_COND_PREP@
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29 #end if
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30 #else:
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31 ## str($input_format) == 'ptorthocs'
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32 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond
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33 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna
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34 #set options_type_cond = orthogroup_fna_cond.options_type_cond
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35 #set options_type = $options_type_cond.options_type
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36 #if str($orthogroup_fna) == 'yes':
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37 #if str(options_type) == 'advanced':
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38 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
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39 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments
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40 @SET_PHYLOGENETIC_TREES_PREP@
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41 #if str($phylogenetic_trees) == 'yes':
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42 @TREE_INFERENCE_COND_PREP@
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43 #end if
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44 #end if
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45 #else:
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46 #if str(options_type) == 'advanced':
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47 @REMOVE_GAPPY_SEQUENCES_COND_PREP@
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48 @SET_PHYLOGENETIC_TREES_PREP@
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49 #if str($phylogenetic_trees) == 'yes':
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50 @TREE_INFERENCE_COND_PREP@
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51 #set sequence_type = $phylogenetic_trees_cond.sequence_type
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52 #end if
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53 #end if
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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
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58 python $__tool_directory__/phylogenomics_analysis.py
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59 --config_dir '$scaffold.fields.path'
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60 --scaffold '$scaffold.fields.path'
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61 --method $method
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62 --num_threads \${GALAXY_SLOTS:-4}
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63
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64 #if str($input_format) == 'ptortho':
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65 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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66 #if str($options_type) == 'advanced':
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67 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
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68 #if str($phylogenetic_trees) == 'yes':
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69 @TREE_INFERENCE_COND_CMD@
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70 --sequence_type 'protein'
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0
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71 #end if
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72 #end if
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73 #else:
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74 ## str($input_format) == 'ptorthocs'
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75 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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76 #if str($orthogroup_fna) == 'yes':
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77 --orthogroup_fna 'true'
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78 #if str(options_type) == 'advanced':
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79 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
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80 #if str($multiple_codon_alignments) == 'yes':
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81 --codon_alignments 'true'
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82 #end if
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83 #if str($phylogenetic_trees) == 'yes':
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84 @TREE_INFERENCE_COND_CMD@
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85 --sequence_type = $phylogenetic_trees_cond.sequence_type
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86 #end if
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0
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87 #end if
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99
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88 #else:
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89 #if str(options_type) == 'advanced':
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90 @REMOVE_GAPPY_SEQUENCES_COND_CMD@
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91 #if str($phylogenetic_trees) == 'yes':
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92 @TREE_INFERENCE_COND_CMD@
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93 --sequence_type = $phylogenetic_trees_cond.sequence_type
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94 #end if
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0
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95 #end if
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96 #end if
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97 #end if
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98
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99 #if str($input_format) == 'ptortho':
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100 --output_ptortho '$output_ptortho'
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101 --output_ptortho_dir '$output_ptortho.files_path'
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42
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102 #else:
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103 --output_ptorthocs '$output_ptorthocs'
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104 --output_ptorthocs_dir '$output_ptorthocs.files_path'
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105 #end if
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105
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106 @OUTPUT_ALN@
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107 @OUTPUT_TREE@
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108 ]]>
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109 </command>
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110 <inputs>
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111 <conditional name="input_format_cond">
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112 <param name="input_format" type="select" label="Select type of data to sub sample">
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113 <option value="ptortho">Precomputed orthologous gene family clusters</option>
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114 <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
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115 </param>
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116 <when value="ptortho">
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117 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
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118 <expand macro="param_scaffold" />
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119 <expand macro="param_method" />
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120 <conditional name="options_type_cond">
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121 <expand macro="param_options_type" />
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122 <when value="basic" />
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123 <when value="advanced">
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124 <expand macro="cond_remove_gappy_sequences" />
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125 <expand macro="cond_phylogenetic_trees_ptortho" />
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126 </when>
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127 </conditional>
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128 </when>
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129 <when value="ptorthocs">
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130 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
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131 <expand macro="param_scaffold" />
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132 <expand macro="param_method" />
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133 <expand macro="cond_orthogroup_fna" />
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0
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134 </when>
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135 </conditional>
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136 </inputs>
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137 <outputs>
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138 <expand macro="output_ptortho" />
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139 <expand macro="output_ptorthocs" />
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140 <expand macro="output_aln" />
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141 <expand macro="output_tree" />
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0
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142 </outputs>
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143 <tests>
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144 <test>
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145 </test>
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146 </tests>
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147 <help>
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148 This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of
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149 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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150 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
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151 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
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152
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153 -----
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154
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155 **Options**
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156
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157 * **Required**
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158
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159 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
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160 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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161 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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162
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163 * **Multiple sequence alignments**
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164
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165 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
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166 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
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167 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
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168 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
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169 - **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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170
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171 * **Phylogenetic trees**
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172
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173 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
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174 - **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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175 - **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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176 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
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177 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
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178
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179 * **MSA quality control**
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180
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181 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
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182 - **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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183 - **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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184
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185 </help>
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186 <expand macro="citations" />
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187 </tool>
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