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annotate quicktree.xml @ 1:5e48f454e36b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit 79d072e206512467e14ffde351a4daaa5cb5165d
author iuc
date Tue, 11 Feb 2025 16:53:26 +0000
parents 1a2cea43d307
children 25c94a3be1b7
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1a2cea43d307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
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1 <tool id="quicktree" name="Quicktree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.5</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
1
5e48f454e36b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit 79d072e206512467e14ffde351a4daaa5cb5165d
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7 <xrefs>
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8 <xref type="bio.tools">quicktree</xref>
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9 </xrefs>
0
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">quicktree</requirement>
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12 <requirement type="package" version="3.4">hmmer</requirement> <!-- for file conversion with esl-reformat-->
1a2cea43d307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
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13 </requirements>
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14 <version_command>quicktree -v</version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16
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17 ## convert alignment to stockholm before quicktree if needed
1a2cea43d307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
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18 #if $input_type.format == "align"
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19 esl-reformat -o input.quicktree stockholm '$input_file' ##--informat a2m
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20 #else
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21 ln -s '$input_file' input.quicktree
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22 #end if
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23
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24 &&
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25
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26 quicktree
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27 #if $input_type.format =="align"
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28 -in a
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29 #else
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30 -in m
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31 #end if
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32 #if $output_type == 'tree_out'
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33 -out t
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34 #else
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35 -out m
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36 #end if
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37 $upgma
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38 $kimura
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39 #if $boot
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40 -boot $boot
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41 #end if
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42 input.quicktree
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43 > '$output_file'
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44
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45 ]]></command>
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46 <inputs>
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47 <conditional name="input_type">
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48 <param name="format" type="select" label="Provide an alignment file or a distance matrix?">
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49 <option value="align">Alignment File</option>
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50 <option value="dist">Distance Matrix</option>
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51 </param>
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52 <when value="align">
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53 <param name="input_file" type="data" format="fasta,stockholm,phylip,txt" label="Alignment file" />
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54 </when>
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55 <when value="dist">
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56 <param name="input_file" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist,txt" label="Distance Matrix" help="A distance matrix in phylip format (see help below for details). Can be a square distance matrix or a lower triangle distance matrix." />
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57 </when>
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58 </conditional>
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59 <param argument="-upgma" type="boolean" truevalue="-upgma" falsevalue="" checked="false" label="Use the UPGMA method to construct the tree" help="ignored for distance matrix outputs"/>
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60 <param argument="-kimura" type="boolean" truevalue="-kimura" falsevalue="" checked="false" label="Use the kimura translation for pairwise distances" help="ignored for distance matrix outputs"/>
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61 <param argument="-boot" type="integer" optional="true" min="0" label="Calcuate bootstrap values with n iterations" help="ignored for distance matrix outputs"/>
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62 <param name="output_type" type="select" multiple="false" label="Choose output format">
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63 <option value="dist_out">Distance Matrix (Phylip format)</option>
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64 <option value="tree_out" selected="true">Tree (Newick format)</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data name="output_file" format="newick" label="${tool.name} on ${on_string}: stockholm format">
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69 <change_format>
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70 <when input="output_type" value="dist_out" format="mothur.dist" />
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71 </change_format>
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72 </data>
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73 </outputs>
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74 <tests>
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75 <test expect_num_outputs="1"><!-- test 1: with fasta input (with reformat) -->
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76 <param name="format" value="align"/>
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77 <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/>
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78 <output name="output_file" file="example.009.AA.newick" ftype="newick"/>
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79 </test>
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80 <test expect_num_outputs="1"><!-- test 2: with stockholm input (no reformat)-->
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81 <param name="format" value="align"/>
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82 <param name="input_file" value="example.009.AA.stockholm" ftype="stockholm"/>
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83 <output name="output_file" file="example.009.AA.newick" ftype="newick"/>
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84 </test>
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85 <test expect_num_outputs="1"><!-- test 3: with clustalw input -->
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86 <param name="format" value="align"/>
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87 <param name="input_file" value="example.011.AA.clw" ftype="txt"/>
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88 <output name="output_file" file="example.011.AA.newick" ftype="newick"/>
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89 </test>
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90 <test expect_num_outputs="1"><!-- test 4: with phylip distance matrix input (lower triangle distance matrix) -->
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91 <param name="format" value="dist"/>
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92 <param name="input_file" value="example.001.AA.dist.lt.phy" ftype="mothur.dist"/>
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93 <output name="output_file" file="example.001.AA.newick" ftype="newick"/>
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94 </test>
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95 <test expect_num_outputs="1"><!-- test 5: with phylip distance matrix input (square distance matrix) -->
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96 <param name="format" value="dist"/>
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97 <param name="input_file" value="example_dist_square_phylip.dist" ftype="mothur.dist"/>
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98 <output name="output_file" file="example_dist_square_phylip.newick" ftype="newick"/>
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99 </test>
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100 <test expect_num_outputs="1"><!-- test 6: with phylip alignment input -->
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101 <param name="format" value="align"/>
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102 <param name="input_file" value="example.011.AA.phy" ftype="phylip"/>
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103 <output name="output_file" file="example.011.AA.align.newick" ftype="newick"/>
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104 </test>
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105 <test expect_num_outputs="1"><!-- test 7: with distance matrix output -->
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106 <param name="format" value="align"/>
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107 <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/>
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108 <param name="output_type" value="dist_out"/>
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109 <output name="output_file" file="example.009.AA.dist" ftype="mothur.dist"/>
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110 </test>
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111 <test expect_num_outputs="1"><!-- test 8: test with all parameters set -->
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112 <param name="format" value="align"/>
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113 <param name="input_file" value="example.011.AA.phy" ftype="phylip"/>
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114 <param name="upgma" value="-upgma"/>
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115 <param name="kimura" value="-kimura"/>
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116 <param name="boot" value="100"/>
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117 <output name="output_file" file="example.011.AA.align.params.newick" ftype="newick"/>
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118 </test>
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119 </tests>
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120 <help><![CDATA[
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121
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122 .. class:: infomark
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123
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124 **What it does**
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125
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126 QuickTree is an efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies
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127 from huge alignments in time less than the age of the universe.
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128
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129
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130 **Input**
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131
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132 QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. The former should be in PHYLIP format. The latter should be in Stockholm format, which is the native alignment format for the Pfam database.
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133
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134 Alignments can be supplied in various other formats (fasta, phylip, clustalw, pfam, psiblast, selex) and will be converted to Stockholm format with the esl-reformat program,
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135 which is part of the HMMer package (hmmer.org).
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136
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137 **Output**
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138
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139 Quicktree will output either a distance matrix (in PHYLIP format, square distance matrix) or a Newick tree.
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140
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141
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142 **File Formats**
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143
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144 The **distance matrix** input should be in phylip format, it can be a square matrix or a lower triangle matrix.
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145 The distance matrix output by quicktree will be a square matrix.
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146
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147 Example square distance matrix in phylip format::
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148
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149 5
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150 Alpha 0.000 1.000 2.000 3.000 3.000
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151 Beta 1.000 0.000 2.000 3.000 3.000
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152 Gamma 2.000 2.000 0.000 3.000 3.000
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153 Delta 3.000 3.000 3.000 0.000 1.000
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154 Epsilon 3.000 3.000 3.000 1.000 0.000
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155
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156 Example of a lower triangle matrix::
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157
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158 7
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159 Mouse
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160 Bovine 1.7043
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161 Lemur 2.0235 1.1901
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162 Orang 2.0593 1.2005 1.5356
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163 Gorilla 1.6664 1.3460 1.4577 1.5935
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164 Chimp 1.7320 1.3757 1.7803 1.7119 1.0635
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165 Human 1.7101 1.3956 1.6661 1.7599 1.0557 0.6933
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166
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167
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168 * For more details about the PHYLIP distance matrix format, see https://phylipweb.github.io/phylip/doc/distance.html
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169 * For more details about the Newick output format, see https://phylipweb.github.io/phylip/newicktree.html
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170
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171
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172 ]]></help>
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173 <citations>
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174 <citation type="doi">10.1093/oxfordjournals.molbev.a040454</citation>
1a2cea43d307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
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175 </citations>
1a2cea43d307 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
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176 </tool>