Mercurial > repos > xuebing > sharplabtool
comparison tools/hyphy/hyphy_nj_tree_wrapper.xml @ 0:9071e359b9a3
Uploaded
author | xuebing |
---|---|
date | Fri, 09 Mar 2012 19:37:19 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9071e359b9a3 |
---|---|
1 <?xml version="1.1.1"?> | |
2 <tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1"> | |
3 | |
4 <description>Builder</description> | |
5 | |
6 <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric ${GALAXY_DATA_INDEX_DIR}</command> | |
7 | |
8 <inputs> | |
9 <page> | |
10 <param format="fasta" name="input1" type="data" label="Fasta file"/> | |
11 <param name="distance_metric" type="select" label="Distance Model"> | |
12 <option value="TN93">Tamura-Nei (93)</option> | |
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> --> | |
14 <!-- <option value="TN84">Tajima-Nei (84) distance (unequal character frequencies)</option> --> | |
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> --> | |
16 <option value="K2P">Kimura 2 parameter</option> | |
17 <option value="JC69">Jukes-Cantor</option> | |
18 <!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> --> | |
19 <!-- <option value="p_Distance">Number of observed substitutions per site</option> --> | |
20 <!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> --> | |
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> --> | |
22 </param> | |
23 </page> | |
24 </inputs> | |
25 <outputs> | |
26 <data name="out_file1" format="tabular" /> | |
27 <data name="out_file2" format="pdf" /> | |
28 </outputs> | |
29 <requirements> | |
30 <requirement type="binary">ps2pdf</requirement> | |
31 </requirements> | |
32 <tests> | |
33 <test> | |
34 <param name="input1" value="nj_tree_inp.fasta"/> | |
35 <param name="distance_metric" value="TN93"/> | |
36 <output name="out_file1" file="nj_tree_newick_out.tabular"/> | |
37 <output name="out_file2" file="nj_tree_pdf_out.pdf"/> | |
38 </test> | |
39 </tests> | |
40 <help> | |
41 This tool takes a single or multiple FASTA alignment file and builds Neighbor Joining Trees using HYPHY_, a maximum likelihood analyses package. | |
42 | |
43 .. _HYPHY: http://www.hyphy.org | |
44 </help> | |
45 </tool> | |
46 |