Mercurial > repos > miller-lab > genome_diversity
annotate phylogenetic_tree.xml @ 5:8a1147101f85
added 3rd party software
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 10 Apr 2012 12:49:47 -0400 |
| parents | 7a94f11fe71f |
| children | e29f4d801bb0 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_phylogenetic_tree" name="Phylogenetic" version="1.0.0"> |
| 2 <description>tree</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
| 5 phylogenetic_tree.py "$input" | |
| 6 #if $individuals.choice == '0' | |
| 7 "all_individuals" | |
| 8 #else if $individuals.choice == '1' | |
| 9 "$p1_input" | |
| 10 #end if | |
|
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7a94f11fe71f
change output.extra_files_path to output.files_path
Richard Burhans <burhans@bx.psu.edu>
parents:
0
diff
changeset
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11 "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality" |
| 0 | 12 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') |
| 13 "none" | |
| 14 #else | |
| 15 "$input.metadata.dbkey" | |
| 16 #end if | |
| 17 "$data_source" | |
| 18 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) | |
| 19 #if $draw_tree_options == '' | |
| 20 "" | |
| 21 #else | |
| 22 "-$draw_tree_options" | |
| 23 #end if | |
| 24 #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 25 #set $arg = '%s:%s' % ($individual_col, $individual_name) | |
| 26 "$arg" | |
| 27 #end for | |
| 28 </command> | |
| 29 | |
| 30 <inputs> | |
| 31 <param name="input" type="data" format="wsf" label="SNP table" /> | |
| 32 | |
| 33 <conditional name="individuals"> | |
| 34 <param name="choice" type="select" label="Individuals"> | |
| 35 <option value="0" selected="true">All</option> | |
| 36 <option value="1">Individuals in a population</option> | |
| 37 </param> | |
| 38 <when value="0" /> | |
| 39 <when value="1"> | |
| 40 <param name="p1_input" type="data" format="ind" label="Population individuals" /> | |
| 41 </when> | |
| 42 </conditional> | |
| 43 | |
| 44 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum coverage" help="Note: Minimum coverage and Minimum quality cannot both be 0" /> | |
| 45 | |
| 46 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum quality" help="Note: Minimum coverage and Minimum quality cannot both be 0" /> | |
| 47 | |
| 48 <param name="include_reference" type="select" format="integer" label="Include reference sequence"> | |
| 49 <option value="1" selected="true">Yes</option> | |
| 50 <option value="0">No</option> | |
| 51 </param> | |
| 52 | |
| 53 <param name="data_source" type="select" format="integer" label="Data source"> | |
| 54 <option value="0" selected="true">sequence coverage</option> | |
| 55 <option value="1">estimated genotype</option> | |
| 56 </param> | |
| 57 | |
| 58 <param name="branch_style" type="select" display="radio"> | |
| 59 <label>Branch type</label> | |
| 60 <option value="" selected="true">square</option> | |
| 61 <option value="d">diagonal</option> | |
| 62 </param> | |
| 63 | |
| 64 <param name="scale_style" type="select" display="radio"> | |
| 65 <label>Draw branches to scale</label> | |
| 66 <option value="" selected="true">yes</option> | |
| 67 <option value="s">no</option> | |
| 68 </param> | |
| 69 | |
| 70 <param name="length_style" type="select" display="radio"> | |
| 71 <label>Show branch lengths</label> | |
| 72 <option value="" selected="true">yes</option> | |
| 73 <option value="b">no</option> | |
| 74 </param> | |
| 75 | |
| 76 <param name="layout_style" type="select" display="radio"> | |
| 77 <label>Tree layout</label> | |
| 78 <option value="" selected="true">horizontal</option> | |
| 79 <option value="v">vertical</option> | |
| 80 </param> | |
| 81 </inputs> | |
| 82 | |
| 83 <outputs> | |
| 84 <data name="output" format="html" /> | |
| 85 </outputs> | |
| 86 | |
| 87 <tests> | |
| 88 <test> | |
| 89 <param name="input" value="test_in/sample.wsf" ftype="wsf" /> | |
| 90 <param name="choice" value="0" /> | |
| 91 <param name="minimum_coverage" value="3" /> | |
| 92 <param name="minimum_quality" value="30" /> | |
| 93 <param name="data_source" value="0" /> | |
| 94 <param name="branch_style" value="" /> | |
| 95 <param name="scale_style" value="" /> | |
| 96 <param name="length_style" value="" /> | |
| 97 <param name="layout_style" value="" /> | |
| 98 <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2"> | |
| 99 <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" /> | |
| 100 <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" /> | |
| 101 <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" /> | |
| 102 <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" /> | |
| 103 <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/> | |
| 104 </output> | |
| 105 </test> | |
| 106 </tests> | |
| 107 | |
| 108 <help> | |
| 109 **What it does** | |
| 110 | |
| 111 This tool uses a SNP table to determine a kind of "genetic distance" between | |
| 112 each pair of individuals. Optionally, that information can be used to | |
| 113 produce a tree-shaped figure that depicts how the individuals are related, | |
| 114 either as a text file in a common format, called NEWICK, or as a picture. | |
| 115 The user specifies the following inputs to the tool. | |
| 116 | |
| 117 SNP table | |
| 118 | |
| 119 Individuals | |
| 120 By default, all individuals are included in the analysis; an option | |
| 121 is to analyze only a subset of individuals that has been specified | |
| 122 using the tool to "Select individuals from a SNP table". | |
| 123 | |
| 124 Minimum coverage | |
| 125 For each pair of individuals, the tool looks for informative SNPs, i.e., | |
| 126 where the sequence data for both individuals is adequate according to | |
| 127 some criterion. Specifying, say, 7 for this option instructs the tool | |
| 128 to consider only SNPs with coverage at least 7 in both individuals | |
| 129 when estimating their "genetic distance". | |
| 130 | |
| 131 Minimum quality | |
| 132 Specifying, say, 37 for this option instructs the tool to consider | |
| 133 only SNPs with SAMtools quality value at least 37 in both individuals | |
| 134 when estimating their "genetic distance". | |
| 135 | |
| 136 Minimum number of informative SNPs | |
| 137 This option instructs the tool to terminate execution if at least one | |
| 138 pair of individuals does not have a required number of informative SNPs. | |
| 139 | |
| 140 Include reference sequence | |
| 141 For SNP tables with a reference sequence, the user can ask that the | |
| 142 reference be indicated in the tree, to help with rooting it. If the | |
| 143 SNP table has no reference sequence, this option has no effect. | |
| 144 | |
| 145 Data source | |
| 146 The genetic distance between two individuals at a given SNP can | |
| 147 be estimated two ways. One method is to use the absolute value of | |
| 148 difference in the frequency of the first allele (equivalently: the | |
| 149 second allele). For instance, if the first individual has 5 reads of | |
| 150 each allele and the second individual has respectively 3 and 6 reads, | |
| 151 then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that | |
| 152 SNP. The other approach is to use the SAMtools genotypes to estimate | |
| 153 the difference in the number of occurrences of the first allele. | |
| 154 For instance, if the two genotypes are 2 and 1, i.e., the individuals | |
| 155 are estimated to have respectively 2 and 1 occurrences of the first | |
| 156 allele at this location, then the distance is 1 (the absolute value | |
| 157 of the difference of the two numbers). | |
| 158 | |
| 159 Output format | |
| 160 There are three options, as described above. | |
| 161 | |
| 162 **Acknowledgments** | |
| 163 | |
| 164 To convert the distance matrix to a NEWICK-formatted tree, we use the QuickTree program, downloaded from: http://www.sanger.ac.uk/resources/software/quicktree/ | |
| 165 | |
| 166 To draw the tree, we use the program draw_tree, downloaded from: http://compgen.bscb.cornell.edu/phast/ | |
| 167 </help> | |
| 168 </tool> |