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/tools/hyphy/hyphy_nj_tree_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 46 lines | 34 code | 5 blank | 7 comment | 0 complexity | 71b6b7809637f4fdbbea69688e655fd2 MD5 | raw file
 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>
41This 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