Mercurial > repos > miller-lab > genome_diversity
comparison phylogenetic_tree.xml @ 24:248b06e86022
Added gd_genotype datatype. Modified tools to support new datatype.
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Tue, 28 May 2013 16:24:19 -0400 |
parents | f04f40a36cc8 |
children | 8997f2ca8c7a |
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23:66a183c44dd5 | 24:248b06e86022 |
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1 <tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.0.0"> | 1 <tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0"> |
2 <description>: Show genetic relationships among individuals</description> | 2 <description>: Show genetic relationships among individuals</description> |
3 | 3 |
4 <command interpreter="python"> | 4 <command interpreter="python"> |
5 phylogenetic_tree.py "$input" | 5 phylogenetic_tree.py "$input" "$output" "$output.files_path" |
6 | |
7 #if $input_type.choice == '0' | |
8 "gd_snp" | |
9 #if $input_type.data_source.choice == '0' | |
10 "sequence_coverage" | |
11 "$input_type.data_source.minimum_coverage" | |
12 "$input_type.data_source.minimum_quality" | |
13 #else if $input_type.data_source.choice == '1' | |
14 "estimated_genotype" | |
15 #end if | |
16 #else if $input_type.choice == '1' | |
17 "gd_genotype" | |
18 #end if | |
19 | |
6 #if $individuals.choice == '0' | 20 #if $individuals.choice == '0' |
7 "all_individuals" | 21 "all_individuals" |
8 #else if $individuals.choice == '1' | 22 #else if $individuals.choice == '1' |
9 "$p1_input" | 23 "$individuals.p1_input" |
10 #end if | 24 #end if |
11 "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality" | 25 |
12 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') | 26 #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') |
13 "none" | 27 "none" |
14 #else | 28 #else |
15 "$input.metadata.dbkey" | 29 "$input.metadata.dbkey" |
16 #end if | 30 #end if |
17 "$data_source" | 31 |
18 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) | 32 #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) |
19 #if $draw_tree_options == '' | 33 #if $draw_tree_options == '' |
20 "" | 34 "" |
21 #else | 35 #else |
22 "-$draw_tree_options" | 36 "-$draw_tree_options" |
23 #end if | 37 #end if |
38 | |
24 #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | 39 #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) | 40 #set $arg = '%s:%s' % ($individual_col, $individual_name) |
26 "$arg" | 41 "$arg" |
27 #end for | 42 #end for |
28 </command> | 43 </command> |
29 | 44 |
30 <inputs> | 45 <inputs> |
31 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> | 46 <conditional name="input_type"> |
47 <param name="choice" type="select" format="integer" label="Input format"> | |
48 <option value="0" selected="true">gd_snp</option> | |
49 <option value="1">gd_genotype</option> | |
50 </param> | |
51 <when value="0"> | |
52 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> | |
53 | |
54 <conditional name="data_source"> | |
55 <param name="choice" type="select" format="integer" label="Distance metric"> | |
56 <option value="0">sequence coverage</option> | |
57 <option value="1" selected="true">estimated genotype</option> | |
58 </param> | |
59 <when value="0"> | |
60 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" /> | |
61 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality" | |
62 help="Note: minimum coverage and minimum quality cannot both be 0" /> | |
63 </when> | |
64 <when value="1"/> | |
65 </conditional> | |
66 </when> | |
67 <when value="1"> | |
68 <param name="input" type="data" format="gd_genotype" label="Genotype dataset" /> | |
69 </when> | |
70 </conditional> | |
32 | 71 |
33 <conditional name="individuals"> | 72 <conditional name="individuals"> |
34 <param name="choice" type="select" label="Compute for"> | 73 <param name="choice" type="select" label="Compute for"> |
35 <option value="0" selected="true">All individuals</option> | 74 <option value="0" selected="true">All individuals</option> |
36 <option value="1">Individuals in a population</option> | 75 <option value="1">Individuals in a population</option> |
39 <when value="1"> | 78 <when value="1"> |
40 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> | 79 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> |
41 </when> | 80 </when> |
42 </conditional> | 81 </conditional> |
43 | 82 |
44 <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" /> | |
45 | |
46 <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality" | |
47 help="Note: minimum coverage and minimum quality cannot both be 0" /> | |
48 | |
49 <param name="include_reference" type="select" format="integer" label="Include reference sequence"> | 83 <param name="include_reference" type="select" format="integer" label="Include reference sequence"> |
50 <option value="1" selected="true">Yes</option> | 84 <option value="1" selected="true">Yes</option> |
51 <option value="0">No</option> | 85 <option value="0">No</option> |
52 </param> | |
53 | |
54 <param name="data_source" type="select" format="integer" label="Distance metric"> | |
55 <option value="0" selected="true">sequence coverage</option> | |
56 <option value="1">estimated genotype</option> | |
57 </param> | 86 </param> |
58 | 87 |
59 <param name="branch_style" type="select" display="radio"> | 88 <param name="branch_style" type="select" display="radio"> |
60 <label>Branch type</label> | 89 <label>Branch type</label> |
61 <option value="" selected="true">square</option> | 90 <option value="" selected="true">square</option> |
108 | 137 |
109 <help> | 138 <help> |
110 | 139 |
111 **Dataset formats** | 140 **Dataset formats** |
112 | 141 |
113 The input dataset is in gd_snp_ format. | 142 The input dataset is in gd_snp_ or gd_genotype_ format. |
114 The output is a composite dataset, containing the tree in both text (Newick_) | 143 The output is a composite dataset, containing the tree in both text (Newick_) |
115 and PostScript formats, as well as supplemental text information. | 144 and PostScript formats, as well as supplemental text information. |
116 (`Dataset missing?`_) | 145 (`Dataset missing?`_) |
117 | 146 |
118 .. _gd_snp: ./static/formatHelp.html#gd_snp | 147 .. _gd_snp: ./static/formatHelp.html#gd_snp |
148 .. _gd_genotype: ./static/formatHelp.html#gd_genotype | |
119 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html | 149 .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html |
120 .. _Dataset missing?: ./static/formatHelp.html | 150 .. _Dataset missing?: ./static/formatHelp.html |
121 | 151 |
122 ----- | 152 ----- |
123 | 153 |