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1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.0">
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2 <description>builds gene family phylogenetic trees</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_gene_family_phylogeny_builder" />
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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 tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
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12 #set tree_inference = $tree_inference_cond.tree_inference
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13 #if str($tree_inference) == 'raxml':
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14 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
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15 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
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16 #if str($rooting_order_file) == 'yes':
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17 #set rooting_order = $rooting_order_file_cond.rooting_order
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18 #end if
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19 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
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20 #end if
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21
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22 python $__tool_directory__/gene_family_phylogeny_builder.py
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23 --orthogroup_aln '$input_aln.extra_files_path'
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24 --scaffold '$scaffold.fields.path'
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25 --config_dir '$scaffold.fields.path'
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26 --method $method
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27 --tree_inference $tree_inference
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28 #if str($tree_inference) == 'raxml':
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29 #if str($rooting_order_file) == 'yes':
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30 --rooting_order '$rooting_order'
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31 ## No else block needed here because the default rooting_order
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32 ## configuration will be used if the --rooting_order flag is missing.
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33 #end if
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34 --bootstrap_replicates $bootstrap_replicates
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35 #end if
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36 --min_orthogroup_size $min_orthogroup_size
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37 --max_orthogroup_size $max_orthogroup_size
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38 --num_threads \${GALAXY_SLOTS:-4}
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39 #if str($input_format) == 'ptalign':
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40 --alignment_type 'aln'
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41 --sequence_type 'protein'
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42 #else if str($input_format) == 'ptalignca':
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43 --alignment_type 'aln'
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44 --sequence_type $input_format_cond.sequence_type
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45 #else if str($input_format) == 'ptalignfiltered':
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46 --alignment_type 'filter'
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47 --sequence_type 'protein'
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48 #else if str($input_format) == 'ptalignfilteredca':
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49 --alignment_type 'filter'
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50 --sequence_type $input_format_cond.sequence_type
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51 #else if str($input_format) == 'ptaligntrimmed':
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52 --alignment_type 'trim'
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53 --sequence_type 'protein'
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54 #else if str($input_format) == 'ptaligntrimmedca':
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55 --alignment_type 'trim'
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56 --sequence_type $input_format_cond.sequence_type
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57 #end if
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58 --output '$output_pttree'
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59 --output_dir '$output_pttree.files_path'
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60 ]]>
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61 </command>
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62 <inputs>
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63 <conditional name="input_format_cond">
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64 <param name="input_format" type="select" label="Select type of data">
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65 <option value="ptalign">Aligned gene family sequences</option>
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66 <option value="ptalignca">Aligned gene family sequences with codon alignments</option>
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67 <option value="ptalignfiltered">Filtered aligned gene family sequences</option>
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68 <option value="ptalignfilteredca">Filtered aligned gene family sequences with codon alignments</option>
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69 <option value="ptaligntrimmed">Trimmed aligned gene family sequences</option>
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70 <option value="ptaligntrimmedca">Trimmed aligned gene family sequences with codon alignments</option>
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71 </param>
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72 <when value="ptalign">
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73 <param name="input_ptalign" format="ptalign" type="data" label="Aligned gene family sequences">
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74 <validator type="empty_files_path" />
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75 </param>
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76 </when>
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77 <when value="ptalignca">
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78 <param name="input_ptalignca" format="ptalignca" type="data" label="Aligned gene family sequences with codon alignments">
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79 <validator type="empty_files_path" />
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80 </param>
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81 <expand macro="param_sequence_type" />
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82 </when>
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83 <when value="ptalignfiltered">
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84 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered aligned gene family sequences">
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85 <validator type="empty_files_path" />
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86 </param>
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87 </when>
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88 <when value="ptalignfilteredca">
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89 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered aligned gene family sequences with codon alignments">
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90 <validator type="empty_files_path" />
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91 </param>
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92 <expand macro="param_sequence_type" />
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93 </when>
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94 <when value="ptaligntrimmed">
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95 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed aligned gene family sequences">
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96 <validator type="empty_files_path" />
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97 </param>
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98 </when>
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99 <when value="ptaligntrimmedca">
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100 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed aligned gene family sequences with codon alignments">
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101 <validator type="empty_files_path" />
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102 </param>
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103 <expand macro="param_sequence_type" />
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104 </when>
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105 </conditional>
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106 <expand macro="param_scaffold" />
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107 <expand macro="param_method" />
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108 <conditional name="tree_inference_cond">
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109 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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110 <option value="raxml" selected="true">RAxML</option>
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111 <option value="fasttree">FastTree</option>
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112 </param>
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113 <when value="raxml">
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114 <conditional name="rooting_order_file_cond">
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115 <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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116 <option value="no" selected="true">No</option>
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117 <option value="yes">Yes</option>
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118 </param>
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119 <when value="no" />
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120 <when value="yes">
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121 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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122 </when>
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123 </conditional>
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124 <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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125 </when>
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126 <when value="fasttree" />
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127 </conditional>
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128 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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129 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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130 </inputs>
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131 <outputs>
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132 <data name="output_pttree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
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133 </outputs>
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134 <tests>
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135 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
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136 <test>
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137 </test>
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138 -->
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139 </tests>
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140 <help>
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141 This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of
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142 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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143 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
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144 **GeneFamilyAligner** tool.
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145
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146 -----
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147
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148 **Required options**
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149
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150 **Other options**
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151
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152 </help>
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153 <citations>
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154 <expand macro="citation1" />
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155 <expand macro="citations2to4" />
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156 </citations>
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157 </tool>
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