[2] | 1 | <?xml version="1.1.1"?> |
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| 2 | <tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1"> |
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| 3 | |
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| 4 | <description>Builder</description> |
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| 5 | |
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| 6 | <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric ${GALAXY_DATA_INDEX_DIR}</command> |
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| 7 | |
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| 8 | <inputs> |
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| 9 | <page> |
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| 10 | <param format="fasta" name="input1" type="data" label="Fasta file"/> |
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| 11 | <param name="distance_metric" type="select" label="Distance Model"> |
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| 12 | <option value="TN93">Tamura-Nei (93)</option> |
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| 13 | <!-- <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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| 14 | <!-- <option value="TN84">Tajima-Nei (84) distance (unequal character frequencies)</option> --> |
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| 15 | <!-- <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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| 16 | <option value="K2P">Kimura 2 parameter</option> |
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| 17 | <option value="JC69">Jukes-Cantor</option> |
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| 18 | <!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> --> |
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| 19 | <!-- <option value="p_Distance">Number of observed substitutions per site</option> --> |
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| 20 | <!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> --> |
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| 21 | <!-- <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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| 22 | </param> |
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| 23 | </page> |
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| 24 | </inputs> |
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| 25 | <outputs> |
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| 26 | <data name="out_file1" format="tabular" /> |
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| 27 | <data name="out_file2" format="pdf" /> |
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| 28 | </outputs> |
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| 29 | <requirements> |
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| 30 | <requirement type="binary">ps2pdf</requirement> |
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| 31 | </requirements> |
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| 32 | <tests> |
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| 33 | <test> |
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| 34 | <param name="input1" value="nj_tree_inp.fasta"/> |
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| 35 | <param name="distance_metric" value="TN93"/> |
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| 36 | <output name="out_file1" file="nj_tree_newick_out.tabular"/> |
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| 37 | <output name="out_file2" file="nj_tree_pdf_out.pdf"/> |
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| 38 | </test> |
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| 39 | </tests> |
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| 40 | <help> |
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| 41 | 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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| 42 | |
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| 43 | .. _HYPHY: http://www.hyphy.org |
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| 44 | </help> |
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| 45 | </tool> |
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| 46 | |
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