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1 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="1.0.0">
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2 <description>pipeline</description>
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3 <requirements>
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4 <requirement type="package" version="0.2">plant_tribes_phylogenomics_analysis</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <!-- In case the return code has not been set properly check stderr too -->
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10 <regex match="Error:" />
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11 <regex match="Exception:" />
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12 </stdio>
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13 <command>
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14 <![CDATA[
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3
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15 #import os
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16 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
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17 #set dest_dir = $output.extra_files_path
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18 mkdir -p $dest_dir &&
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19 PhylogenomicsAnalysis
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7
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20 --orthogroup_faa "$orthogroup_faa.extra_files_path"
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0
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21 --scaffold "$scaffold"
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22 --method $method
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23 #if str($options_type.options_type_selector) == 'advanced':
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5
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24 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
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0
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25 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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5
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26 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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27 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
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6
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28 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
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7
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29 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
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30 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
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5
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31 #if str($multiple_sequence_alignments_option) == 'create_alignments':
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32 --create_alignments
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5
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33 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
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34 --add_alignments
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5
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35 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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36 --pasta_alignments
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37 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
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38 #end if
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5
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39 #if str($multiple_codon_alignments) == 'yes':
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40 --codon_alignments
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41 #if str($use_corresponding_coding_sequences) == 'yes':
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42 --orthogroup_fna
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43 #end if
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44 --sequence_type $multiple_codon_alignments_cond.sequence_type
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45 #end if
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46 #end if
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47 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
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48 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
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49 #set tree_inference_method = $tree_inference_cond.tree_inference
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50 --tree_inference $tree_inference_method
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51 #if str($tree_inference_method) == 'raxml':
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52 --rooting_order "$tree_inference_cond.rooting_order"
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53 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
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54 #end if
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55 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
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56 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
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57 #end if
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58 #if str($options_type.msa_quality_control_options_cond.msa_quality_control_options) == 'yes':
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59 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
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60 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
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61 #if str($remove_gappy_sequences_cond) == 'yes':
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62 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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63 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
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64 #if str($trim_type_cond.trim_type) == 'automated_trimming':
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65 --automated_trimming
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66 else:
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67 --gap_trimming $trim_type_cond.gap_trimming
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68 #end if
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69 #end if
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70 #end if
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71 #end if
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72 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
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4
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73 --num_threads \${GALAXY_SLOTS:-4}
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74 && echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output
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75 && ls $src_dir >> $output
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76 && mv $src_dir/* $dest_dir
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0
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77 ]]>
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78 </command>
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79 <inputs>
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80 <param name="orthogroup_faa" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
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0
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81 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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82 <options from_data_table="plant_tribes_scaffolds" />
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83 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
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84 </param>
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85 <param name="method" type="select" label="Protein clustering method">
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86 <option value="gfam" selected="true">GFam</option>
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87 <option value="orthofinder">OrthoFinder</option>
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88 <option value="orthomcl">OrthoMCL</option>
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89 </param>
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90 <conditional name="options_type">
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91 <param name="options_type_selector" type="select" label="Options Configuration">
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92 <option value="basic" selected="true">Basic</option>
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93 <option value="advanced">Advanced</option>
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94 </param>
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95 <when value="basic" />
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96 <when value="advanced">
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97 <conditional name="multiple_sequence_alignments_cond">
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98 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
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99 <option value="no" selected="true">No</option>
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100 <option value="yes">Yes</option>
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101 </param>
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102 <when value="no" />
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103 <when value="yes">
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104 <conditional name="multiple_sequence_alignments_option_cond">
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105 <param name="multiple_sequence_alignments_option" label="Select option" type="select" force_select="True">
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106 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
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107 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
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108 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
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109 </param>
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110 <when value="create_alignments"/>
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111 <when value="add_alignments"/>
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112 <when value="pasta_alignments">
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113 <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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114 </when>
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115 </conditional>
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116 <conditional name="multiple_codon_alignments_cond">
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117 <param name="multiple_codon_alignments" label="Construct orthogroup multiple codon alignments?" type="select">
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118 <option value="no" selected="True">No</option>
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119 <option value="yes">Yes</option>
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120 </param>
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121 <when value="yes">
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122 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)">
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123 <option value="protein" selected="true">Amino acid based</option>
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124 <option value="dna">Nucleotide based</option>
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125 </param>
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126
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127
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128 <conditional name="use_corresponding_coding_sequences_cond">
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129 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool">
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130 <option value="no" selected="true">No</option>
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131 <option value="yes">Yes</option>
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132 </param>
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133 <when value="no" />
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134 <when value="yes" />
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135 </conditional>
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136
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137
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138 </when>
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139 <when value="no"/>
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140 </conditional>
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141 </when>
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142 </conditional>
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143 <conditional name="phylogenetic_trees_cond">
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144 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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145 <option value="no" selected="true">No</option>
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146 <option value="yes">Yes</option>
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147 </param>
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148 <when value="no" />
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149 <when value="yes">
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150 <conditional name="tree_inference_cond">
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151 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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152 <option value="raxml" selected="true">RAxML</option>
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153 <option value="fasttree">FastTree</option>
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154 </param>
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155 <when value="raxml">
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156 <param name="rooting_order" format="txt" type="data" label="Select file containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees"/>
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157 <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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158 </when>
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159 <when value="fasttree"/>
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160 </conditional>
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161 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments"/>
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162 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments"/>
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163 </when>
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164 </conditional>
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165 <conditional name="msa_quality_control_options_cond">
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166 <param name="msa_quality_control_options" type="select" label="Set MSA quality control options?">
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167 <option value="no" selected="true">No</option>
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168 <option value="yes">Yes</option>
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169 </param>
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170 <when value="no" />
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171 <when value="yes">
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172 <conditional name="remove_gappy_sequences_cond">
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173 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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174 <option value="no" selected="true">No</option>
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175 <option value="yes">Yes</option>
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176 </param>
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177 <when value="no"/>
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178 <when value="yes">
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179 <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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180 <conditional name="trim_type_cond">
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181 <param name="trim_type" type="select" label="Select process used for gap trimming">
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182 <option value="automated_trimming" selected="true">Trim alignments using trimAl's ML heuristic trimming approach</option>
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183 <option value="gap_trimming">Nucleotide based</option>
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184 </param>
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185 <when value="automated_trimming"/>
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186 <when value="gap_trimming">
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187 <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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188 </when>
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189 </conditional>
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190 </when>
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191 </conditional>
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192 </when>
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193 </conditional>
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194 </when>
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195 </conditional>
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196 </inputs>
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197 <outputs>
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198 <data name="output" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
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199 </outputs>
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200 <tests>
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201 <test>
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202 <param name="input" value="" ftype="fasta" />
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203 <param name="prediction_method" value="transdecoder"/>
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204 <param name="target_gene_family_assembly" value="no"/>
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205 <param name="strand_specific" value="yes"/>
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206 <param name="dereplicate" value="yes"/>
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207 <param name="min_length" value="200"/>
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208 <output_collection name="orthos" type="list">
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209 </output_collection>
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210 </test>
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211 </tests>
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212 <help>
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213 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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214 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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215 analyses, comparing and analyzing the sequences of single genes, or a small number of genes, as well as many other types of data.
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216
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217 -----
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218
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219 **Options**
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220
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221 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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222 * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
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223 * **Protein classification method** - One of blastp, HMMScan or both.
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224 * **SuperOrthogroups MCL clustering** - blastp e-value matrix between all pairs of orthogroups.
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225 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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226 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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227 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
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228
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229 </help>
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230 <citations>
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231 <citation type="bibtex">
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232 @unpublished{None,
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233 author = {None},
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234 title = {None},
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235 year = {None},
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236 eprint = {None},
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237 url = {None}
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238 }</citation>
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239 </citations>
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240 </tool>
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