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Add Quicktree tool
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| categories: | ||
| - Phylogenetics | ||
| description: neighbour-joining phylogenetic inference | ||
| long_description: | | ||
| QuickTree is an efficient implementation of the Neighbor-Joining | ||
| algorithm, capable of reconstructing phylogenies from huge alignments | ||
| homepage_url: https://github.com/khowe/quicktree | ||
| name: quicktree | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree | ||
| type: unrestricted |
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| <tool id="quicktree" name="Quicktree" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | ||
| <description></description> | ||
| <macros> | ||
| <token name="@TOOL_VERSION@">2.5</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| </macros> | ||
| <edam_topics> | ||
| <edam_topic>topic_3293</edam_topic> <!-- phylogenetics --> | ||
| </edam_topics> | ||
| <edam_operations> | ||
| <edam_operation>operation_0540</edam_operation> <!-- Phylogenetic inference (from molecular sequences) --> | ||
| </edam_operations> | ||
| <requirements> | ||
| <requirement type="package" version="@TOOL_VERSION@">quicktree</requirement> | ||
| <requirement type="package" version="3.4">hmmer</requirement> <!-- for file conversion with esl-reformat--> | ||
| </requirements> | ||
| <version_command>quicktree -v</version_command> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| ## convert alignment to stockholm before quicktree if needed | ||
| #if $input_type.format == "align" | ||
| esl-reformat -o input.quicktree stockholm '$input_file' ##--informat a2m | ||
| #else | ||
| ln -s '$input_file' input.quicktree | ||
| #end if | ||
| && | ||
| quicktree | ||
| #if $input_type.format =="align" | ||
| -in a | ||
| #else | ||
| -in m | ||
| #end if | ||
| #if $output_type == 'tree_out' | ||
| -out t | ||
| #else | ||
| -out m | ||
| #end if | ||
| $upgma | ||
| $kimura | ||
| #if $boot | ||
| -boot $boot | ||
| #end if | ||
| input.quicktree | ||
| > '$output_file' | ||
| ]]></command> | ||
| <inputs> | ||
| <conditional name="input_type"> | ||
| <param name="format" type="select" label="Provide an alignment file or a distance matrix?"> | ||
| <option value="align">Alignment File</option> | ||
| <option value="dist">Distance Matrix</option> | ||
| </param> | ||
| <when value="align"> | ||
| <param name="input_file" type="data" format="fasta,stockholm,phylip,txt" label="Alignment file" /> | ||
| </when> | ||
| <when value="dist"> | ||
| <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." /> | ||
| </when> | ||
| </conditional> | ||
| <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"/> | ||
| <param argument="-kimura" type="boolean" truevalue="-kimura" falsevalue="" checked="false" label="Use the kimura translation for pairwise distances" help="ignored for distance matrix outputs"/> | ||
| <param argument="-boot" type="integer" optional="true" min="0" label="Calcuate bootstrap values with n iterations" help="ignored for distance matrix outputs"/> | ||
| <param name="output_type" type="select" multiple="false" label="Choose output format"> | ||
| <option value="dist_out">Distance Matrix (Phylip format)</option> | ||
| <option value="tree_out" selected="true">Tree (Newick format)</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output_file" format="newick" label="${tool.name} on ${on_string}: stockholm format"> | ||
| <change_format> | ||
| <when input="output_type" value="dist_out" format="mothur.dist" /> | ||
| </change_format> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs="1"><!-- test 1: with fasta input (with reformat) --> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/> | ||
| <output name="output_file" file="example.009.AA.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 2: with stockholm input (no reformat)--> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.009.AA.stockholm" ftype="stockholm"/> | ||
| <output name="output_file" file="example.009.AA.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 3: with clustalw input --> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.011.AA.clw" ftype="txt"/> | ||
| <output name="output_file" file="example.011.AA.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 4: with phylip distance matrix input (lower triangle distance matrix) --> | ||
| <param name="format" value="dist"/> | ||
| <param name="input_file" value="example.001.AA.dist.lt.phy" ftype="mothur.dist"/> | ||
| <output name="output_file" file="example.001.AA.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 5: with phylip distance matrix input (square distance matrix) --> | ||
| <param name="format" value="dist"/> | ||
| <param name="input_file" value="example_dist_square_phylip.dist" ftype="mothur.dist"/> | ||
| <output name="output_file" file="example_dist_square_phylip.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 6: with phylip alignment input --> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.011.AA.phy" ftype="phylip"/> | ||
| <output name="output_file" file="example.011.AA.align.newick" ftype="newick"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 7: with distance matrix output --> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.009.AA.fasta" ftype="fasta"/> | ||
| <param name="output_type" value="dist_out"/> | ||
| <output name="output_file" file="example.009.AA.dist" ftype="mothur.dist"/> | ||
| </test> | ||
| <test expect_num_outputs="1"><!-- test 8: test with all parameters set --> | ||
| <param name="format" value="align"/> | ||
| <param name="input_file" value="example.011.AA.phy" ftype="phylip"/> | ||
| <param name="upgma" value="-upgma"/> | ||
| <param name="kimura" value="-kimura"/> | ||
| <param name="boot" value="100"/> | ||
| <output name="output_file" file="example.011.AA.align.params.newick" ftype="newick"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| .. class:: infomark | ||
| **What it does** | ||
| QuickTree is an efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies | ||
| from huge alignments in time less than the age of the universe. | ||
| **Input** | ||
| 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. | ||
| 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, | ||
| which is part of the HMMer package (hmmer.org). | ||
| **Output** | ||
| Quicktree will output either a distance matrix (in PHYLIP format, square distance matrix) or a Newick tree. | ||
| **File Formats** | ||
| The **distance matrix** input should be in phylip format, it can be a square matrix or a lower triangle matrix. | ||
| The distance matrix output by quicktree will be a square matrix. | ||
| Example square distance matrix in phylip format:: | ||
| 5 | ||
| Alpha 0.000 1.000 2.000 3.000 3.000 | ||
| Beta 1.000 0.000 2.000 3.000 3.000 | ||
| Gamma 2.000 2.000 0.000 3.000 3.000 | ||
| Delta 3.000 3.000 3.000 0.000 1.000 | ||
| Epsilon 3.000 3.000 3.000 1.000 0.000 | ||
| Example of a lower triangle matrix:: | ||
| 7 | ||
| Mouse | ||
| Bovine 1.7043 | ||
| Lemur 2.0235 1.1901 | ||
| Orang 2.0593 1.2005 1.5356 | ||
| Gorilla 1.6664 1.3460 1.4577 1.5935 | ||
| Chimp 1.7320 1.3757 1.7803 1.7119 1.0635 | ||
| Human 1.7101 1.3956 1.6661 1.7599 1.0557 0.6933 | ||
| * For more details about the PHYLIP distance matrix format, see https://phylipweb.github.io/phylip/doc/distance.html | ||
| * For more details about the Newick output format, see https://phylipweb.github.io/phylip/newicktree.html | ||
| ]]></help> | ||
| <citations> | ||
| <citation type="doi">10.1093/oxfordjournals.molbev.a040454</citation> | ||
| </citations> | ||
| </tool> |
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