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Add Quicktree tool #6583

Merged
merged 12 commits into from
Nov 25, 2024
18 changes: 12 additions & 6 deletions tools/quicktree/quicktree.xml
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ input.quicktree
<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,txt" label="Distance Matrix" />
<param name="input_file" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dixt,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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  • mothur.square.dixt -> mothur.square.dist
  • txt can / should we replace this by tabular? Or at least add it?

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should we replace this by tabular

I answer this myself: No :)

</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"/>
Expand Down Expand Up @@ -90,23 +90,28 @@ input.quicktree
<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 -->
<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.phy" ftype="mothur.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 alignment input -->
<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 6: with distance matrix output -->
<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 7: test with all parameters set -->
<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"/>
Expand All @@ -133,6 +138,7 @@ Alignments can be supplied in various other formats (fasta, phylip, clustalw, pf
which is part of the HMMer package (hmmer.org).



**Output**

Quicktree will output either a distance matrix (in PHYLIP format) or a Newick tree.
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