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44 lines
2.5 KiB
XML
44 lines
2.5 KiB
XML
<?xml version="1.0"?>
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<tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1">
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<description>Builder</description>
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<command interpreter="python2.4">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric</command>
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<inputs>
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<page>
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<param format="fasta" name="input1" type="data" label="Fasta file"/>
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<param name="distance_metric" type="select" label="Distance Model">
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<option value="TN93">Tamura-Nei (93)</option>
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<!-- <option value="TN93_RV">Tamura-Nei (93) distance and rate variation (unequal character frequencies, A->G, C->T and transversional bias corrections, gamma distributed rate variation from site to site)</option> -->
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<!-- <option value="TN84">Tajima-Nei (84) distance (unequal character frequencies)</option> -->
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<!-- <option value="K2P_RV">Kimura 2 parameter and rate variation (equal character frequencies, transition/trasversion bias correction, gamma distributed rate variation from site to site)</option> -->
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<option value="K2P">Kimura 2 parameter</option>
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<option value="JC69">Jukes-Cantor</option>
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<!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> -->
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<!-- <option value="p_Distance">Number of observed substituions per site</option> -->
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<!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> -->
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<!-- <option value="Unaligned_LZ_FR">Distance measure for unaligned sequences based on Lempel Ziv measure of information content using the best choice forward and reverse string orientations</option> -->
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</param>
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</page>
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</inputs>
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<outputs>
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<data name="out_file1" format="tabular" />
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<data name="out_file2" format="pdf" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="cf_maf2fasta.dat"/>
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<param name="distance_metric" value="TN93"/>
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<output name="out_file1" file="nj_tree_newick_out.dat"/>
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<!-- <output name="out_file2" file="nj_tree_pdf_out.dat"/> generated tests can currently check only one file-->
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</test>
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</tests>
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<help>
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This tool takes a single or multiple FASTA alignment file and builds Neighbor Joining Trees using HYPHY_, a maximum likelihood analyses package.
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.. _HYPHY: http://www.hyphy.org
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</help>
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</tool>
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