Mercurial > repos > iuc > quicktree
diff quicktree.xml @ 0:1e89a460d1bd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quicktree commit ba1e44dfaf0a986252e2fef60a831b819647f25e
| author | iuc |
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| date | Mon, 25 Nov 2024 13:13:10 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/quicktree.xml Mon Nov 25 13:13:10 2024 +0000 @@ -0,0 +1,179 @@ +<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>