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annotate phykit_tree_based.xml @ 0:37b049bf729a draft

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"planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Mon, 28 Mar 2022 16:23:18 +0000
parents
children 1ac6ee298657
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1 <tool id="phykit_tree_based" name="PhyKit - Tree-based functions" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="1.11.7">phykit</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6
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7 #if $tools.tool_selector == "evolutionary_rate"
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8 phykit evolutionary_rate $tools.input1 > $evo_rate;
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9 #elif $tools.tool_selector == "patristic_distances"
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10 phykit patristic_distances $tools.verbose $tools.input1 > $patristic_distances;
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11 #elif $tools.tool_selector == "prune_tree"
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12 phykit prune_tree $tools.input1 $tools.input2
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13 -o 'out.pruned'
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14 $tools.keep;
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15 cp out.pruned ${pruned_tree_out};
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16 #elif $tools.tool_selector == "robinson_foulds_distance"
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17 phykit robinson_foulds_distance $tools.input1 $tools.input2 > $rf_distance;
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18 #elif $tools.tool_selector == "root_tree"
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19 phykit root_tree $tools.input1
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20 -r $tools.input2
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21 -o 'out.rooted';
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22 cp out.rooted ${rooted_tree};
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23 #end if
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24
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25 ]]></command>
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26 <inputs>
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27 <conditional name="tools">
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28 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
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29 <option value="evolutionary_rate">Calculate a tree-based estimation of the evolutionary rate of a gene.</option>
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30 <option value="patristic_distances">Calculate summary statistics among patristic distances in a phylogeny</option>
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31 <option value="prune_tree">Prune tips from a phylogeny</option>
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32 <option value="robinson_foulds_distance">Calculate Robinson-Foulds (RF) distance between two trees</option>
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33 <option value="root_tree">Root phylogeny using user-specified taxa</option>
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34 </param>
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35 <when value="evolutionary_rate">
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36 <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
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37 </when>
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38 <when value="patristic_distances">
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39 <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
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40 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="optional argument to get all distances" />
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41 </when>
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42 <when value="prune_tree">
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43 <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
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44 <param name="input2" type="data" format="text" multiple="false" label="Single column file with the names of the tips to remove from the phylogeny" optional="false" />
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45 <param name="keep" type="boolean" truevalue="--keep" falsevalue="" checked="False" label="Instead of pruning tips in list of taxa, keep them" />
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46 </when>
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47 <when value="robinson_foulds_distance">
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48 <param name="input1" type="data" format="newick" multiple="false" label="Tree 1" optional="false" />
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49 <param name="input2" type="data" format="newick" multiple="false" label="Tree 2" optional="false" />
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50 </when>
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51 <when value="root_tree">
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52 <param name="input1" type="data" format="newick" multiple="false" label="Tree file" optional="false" />
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53 <param name="input2" type="data" format="text" multiple="false" label="Single column file with taxa names to root the phylogeny on" optional="false" />
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54 </when>
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55 </conditional>
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56 </inputs>
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57 <outputs>
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58 <data name="evo_rate" format="txt" label="total tree length divided by the number of terminals.">
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59 <filter>tools['tool_selector']=='evolutionary_rate'</filter>
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60 </data>
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61 <data name="patristic_distances" format="txt" label="summary statistics of all tip-to-tip distances in a phylogeny. With the -v option, the first column will have two taxon names separated by a ‘-‘ followed by the patristic distance. Features will be tab separated.">
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62 <filter>tools['tool_selector']=='patristic_distances'</filter>
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63 </data>
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64 <data name="pruned_tree_out" format="newick" label="Pruned phylogeny">
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65 <filter>tools['tool_selector']=='prune_tree'</filter>
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66 </data>
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67 <data name="rf_distance" format="tabular" label="col 1; the plain RF distance and col 2: the normalized RF distance" >
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68 <filter>tools['tool_selector']=='robinson_foulds_distance'</filter>
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69 </data>
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70 <data name="rooted_tree" format="newick" label="Rooted tree">
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71 <filter>tools['tool_selector']=='root_tree'</filter>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="tool_selector" value="evolutionary_rate" />
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77 <param name="input1" value="12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit.treefile"/>
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78 <output name="evolutionary_rate" file="test_evo_rate.txt"/>
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79 </test>
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80 <test>
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81 <param name="tool_selector" value="patristic_distances" />
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82 <param name="input1" value="tree_simple.tre"/>
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83 <param name="verbose" value="false" />
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84 <output name="patristic_distances" file="test_tree_simple_pd.txt"/>
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85 </test>
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86 <test>
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87 <param name="tool_selector" value="patristic_distances" />
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88 <param name="input1" value="tree_simple.tre"/>
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89 <param name="verbose" value="true" />
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90 <output name="patristic_distances" file="test_tree_simple_pd_verbose.txt"/>
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91 </test>
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92 <test>
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93 <param name="tool_selector" value="prune_tree" />
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94 <param name="input1" value="tree_simple.tre"/>
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95 <param name="input2" value="tree_simple_prune.txt"/>
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96 <param name="keep" value="false" />
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97 <output name="pruned_tree_out" file="tree_simple.pruned"/>
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98 </test>
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99 <test>
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100 <param name="tool_selector" value="prune_tree" />
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101 <param name="input1" value="tree_simple.tre"/>
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102 <param name="input2" value="tree_simple_prune.txt"/>
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103 <param name="keep" value="true" />
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104 <output name="pruned_tree_out" file="tree_simple_keep.pruned"/>
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105 </test>
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106 <test>
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107 <param name="tool_selector" value="robinson_foulds_distance" />
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108 <param name="input1" value="tree_simple.tre"/>
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109 <param name="input2" value="tree_simple_other_topology.tre"/>
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110 <output name="rf_distance" file="test_tree_simple_rfd.txt"/>
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111 </test>
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112 <test>
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113 <param name="tool_selector" value="root_tree" />
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114 <param name="input1" value="tree_simple.tre"/>
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115 <param name="input2" value="tree_simple.outgroup.txt"/>
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116 <output name="rooted_tree" file="tree_simple.tre.rooted"/>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120
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121 Version: 1.11.3
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122 Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096
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123 Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#tree-based-functions
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124 Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675
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125
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126 PhyKIT helps process and analyze multiple sequence alignments and phylogenies.
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127
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128 Generally, all functions are designed to help understand the contents of alignments
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129 (e.g., gc content or the number of parsimony informative sites) and the shape
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130 of trees (e.g., treeness, degree of violation of a molecular clock).
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131
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132 Tree-based commands
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133 ===================
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134 evolutionary_rate (alias: evo_rate)
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135 - reports a tree-based estimation of evolutionary rate for a gene
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136 patristic_distances (alias: pd)
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137 - calculate all pairwise distances between tips in a tree
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138 prune_tree (alias: prune)
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139 - prune taxa from a phylogeny
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140 robinson_foulds_distance (alias: rf_distance; rf_dist; rf)
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141 - calculates Robinson-Foulds distance between two trees
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142 root_tree (alias: root; rt)
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143 - roots tree on user-specified taxa or taxon
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144
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145 ]]></help>
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146 <citations>
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147 <citation type="bibtex">
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148 @misc{githubPhyKIT,
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149 author = {LastTODO, FirstTODO},
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150 year = {TODO},
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151 title = {PhyKIT},
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152 publisher = {GitHub},
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153 journal = {GitHub repository},
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154 url = {https://github.com/JLSteenwyk/PhyKIT},
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155 }</citation>
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156 </citations>
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157 </tool>