Mercurial > repos > iuc > ete_treeviewer

annotate ete-treeviewer.xml @ 0:7a598c88bd46 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit commit d2208e858d6486dd2e832978aca30ca67837cfd6
author iuc
date Tue, 10 Dec 2024 09:55:02 +0000
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7a598c88bd46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit commit d2208e858d6486dd2e832978aca30ca67837cfd6
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1 <tool id="ete_treeviewer" name="ETE tree viewer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>visualize a phylogenetic tree</description>
7a598c88bd46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit commit d2208e858d6486dd2e832978aca30ca67837cfd6
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.1.3</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0567</edam_operation> <!-- phylogenetic tree visualisation -->
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12 </edam_operations>
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13 <xrefs>
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14 <xref type="bio.tools">ete</xref>
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15 </xrefs>
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16 <requirements>
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17 <!--<requirement type="package" version="@TOOL_VERSION@">ete3</requirement>-->
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18 <requirement type="package" version="8.10.1">curl</requirement>
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19 <requirement type="package" version="1.6.1">xmlstarlet</requirement>
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20 <requirement type="package" version="2.58.4">librsvg</requirement>
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21 </requirements>
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22 <command detect_errors="exit_code"><![CDATA[
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23
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24 curl http://etetoolkit.org/get_svg/
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25 -X POST
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26 --retry 10
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27 #if $align.align_choice == 'yes'
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28 -d "tree=\$(cat '$input_tree');fasta=\$(cat '$align.input_alignment');alg_type=$align.alg_type;$ncbitaxa" | xml format - > tree.svg
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29 #else
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30 -d "tree=\$(cat '$input_tree');$ncbitaxa" | xml format - > tree.svg
7a598c88bd46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ete-toolkit commit d2208e858d6486dd2e832978aca30ca67837cfd6
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31 #end if
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32
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33 #if $output_format == 'png'
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34 && rsvg-convert -o tree.png tree.svg
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35 && mv tree.png '$output_tree_image'
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36 #else
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37 && mv tree.svg '$output_tree_image'
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38 #end if
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39
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40 ]]></command>
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41 <inputs>
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42 <param name="input_tree" type="data" format="newick" label="Newick Tree to visualise" />
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43 <conditional name="align">
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44 <param name="align_choice" type="select" label="Add alignment information to image?" help="Will display alignments in the tree view">
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45 <option value="yes">yes</option>
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46 <option value="no" selected="true">no</option>
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47 </param>
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48 <when value="yes">
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49 <param name="input_alignment" type="data" format="fasta" optional="true" label="Multiple Alignment FASTA file" help="If provided, will add alignment visualisation to tree image" />
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50 <param name="alg_type" type="select" multiple="false" label="Alignment display style" help="Will be ignored if no alignment file provided.">
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51 <option value="block">Aligned blocks</option>
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52 <option value="condensed" selected="true">Condensed format</option>
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53 </param>
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54 </when>
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55 <when value="no"/>
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56 </conditional>
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57
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58 <param name="ncbitaxa" type="boolean" checked="true" truevalue="ncbitaxa=true;" falsevalue="" label="Resolve Taxonomic IDs?" help="Use NCBI numeric taxids as leaf names (or in the format TaxID.sequenceName) in your tree." />
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59 <param name="output_format" type="select" multiple="false" label="Format of the output image." help="SVG or PNG">
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60 <option value="svg" selected="true">SVG</option>
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61 <option value="png">PNG</option>
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62 </param>
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63 </inputs>
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64 <outputs>
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65 <data name="output_tree_image" format="svg" label="${tool.name} on ${on_string}: Tree Image">
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66 <change_format>
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67 <when input="output_format" value="png" format="png"/>
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68 </change_format>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test expect_num_outputs="1"><!-- test 1: with NCBI TaxIDs -->
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73 <param name="input_tree" value="quicktree_alignment_VARL_NCBI.tre" ftype="newick"/>
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74 <output name="output_tree_image" file="quicktree_VARL_NCBI.svg" ftype="svg" lines_diff="500" />
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75 </test>
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76 <test expect_num_outputs="1"><!-- test 2: with alignment file -->
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77 <param name="input_tree" value="example-tree-ncbi.tree" ftype="newick"/>
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78 <param name="align_choice" value="yes" />
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79 <param name="input_alignment" value="example-alignment.fa" ftype="fasta"/>
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80 <output name="output_tree_image" ftype="svg">
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81 <assert_contents>
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82 <has_text text="Generated with ETE http://ete.cgenomics.org"/>
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83 <has_text text="Branchiostoma floridae"/>
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84 <has_n_lines min="150000" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test expect_num_outputs="1"><!-- test 3: with aligment style set -->
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89 <param name="input_tree" value="example-tree-ncbi.tree" ftype="newick"/>
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90 <param name="align_choice" value="yes" />
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91 <param name="input_alignment" value="example-alignment.fa" ftype="fasta"/>
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92 <param name="alg_type" value="block"/>
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93 <output name="output_tree_image" ftype="svg">
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94 <assert_contents>
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95 <has_text text="Generated with ETE http://ete.cgenomics.org"/>
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96 <has_text text="Branchiostoma floridae"/>
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97 <has_n_lines min="25000" max="30000" />
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <test expect_num_outputs="1"><!-- test 4: minimal tree, no taxonomy, no alignment -->
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102 <param name="input_tree" value="quicktree_alignment_VARL.tre" ftype="newick"/>
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103 <param name="align_choice" value="no" />
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104 <output name="output_tree_image" file="minimal-tree-out.svg" ftype="svg" lines_diff="0"/>
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105 </test>
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106 <test expect_num_outputs="1"><!-- test 5: png output -->
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107 <param name="input_tree" value="quicktree_alignment_VARL.tre" ftype="newick"/>
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108 <param name="output_format" value="png" />
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109 <output name="output_tree_image" ftype="png" >
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110 <assert_contents>
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111 <has_image_width min="500" />
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112 <has_image_height min="500" />
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113 </assert_contents>
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114 </output>
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115 </test>
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116 </tests>
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117 <help><![CDATA[
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118
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119 .. class:: infomark
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120
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121 **What it does**
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122
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123 This is a tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format). It uses the tree drawing engine implemented in the ETE toolkit, and offers transparent integration with the NCBI taxonomy database. Currently, alignments can be displayed in condensed or block-based format.
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124
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125 **Input**
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126
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127 Input trees should be in Newick format. Optionally a fasta alignment may also be provided. Leaf names in the newick tree should match those in the fasta alignment.
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128
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129 Tip: Use NCBI numeric taxids as leaf names (or in the format TaxID.sequenceName) to get on-the-fly translation of species names and lineages.
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130
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131 For example::
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132
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133 ((6669.DappuP312785:1.24473,(((7739.JGI126010:4.02e-06,7739.JGI126021:0.168081)0.99985:0.848895, [..]
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134
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135 where 66969 and 7739 are NCBI TaXIDs.
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136
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137 **Output**
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138
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139 The tool will output a tree image in SVG or PNG format.
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140
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141 .. image:: $PATH_TO_IMAGES/example-treeview.png
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142 :width: 50%
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143 :alt: example tree image
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144
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145 ]]></help>
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146 <citations>
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147 <citation type="doi">10.1093/molbev/msw046</citation>
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148 </citations>
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149 </tool>