Mercurial > repos > yusuf > combine_hgvs_annotations
comparison CombineHGVSAnnotations.xml @ 0:baf1543e8ae1 default tip
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author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:27:49 -0600 |
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-1:000000000000 | 0:baf1543e8ae1 |
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1 <?xml version="1.0"?> | |
2 | |
3 <tool id="hgvs_combine_1" name="Combine multiple HGVS tables"> | |
4 <description> to find concordant and discordant variant calls</description> | |
5 <version_string>combine_hgvs_tables -v</version_string> | |
6 <command interpreter="perl">combine_hgvs_tables -q $collapse $output_hgvs_table | |
7 $params.input_hgvs_table_name1 $params.input_hgvs_table1 | |
8 $params.input_hgvs_table_name2 $params.input_hgvs_table2 | |
9 #if $int($str($params.source_select)) > 2: | |
10 $params.input_hgvs_table_name3 $params.input_hgvs_table3 | |
11 #end if | |
12 #if $int($str($params.source_select)) > 3: | |
13 $params.input_hgvs_table_name4 $params.input_hgvs_table4 | |
14 #end if | |
15 #if $int($str($params.source_select)) > 4: | |
16 $params.input_hgvs_table_name5 $params.input_hgvs_table5 | |
17 #end if | |
18 #if $int($str($params.source_select)) > 5: | |
19 $params.input_hgvs_table_name6 $params.input_hgvs_table6 | |
20 #end if | |
21 #if $int($str($params.source_select)) > 6: | |
22 $params.input_hgvs_table_name7 $params.input_hgvs_table7 | |
23 #end if | |
24 #if $int($str($params.source_select)) > 7: | |
25 $params.input_hgvs_table_name8 $params.input_hgvs_table8 | |
26 #end if | |
27 #if $int($str($params.source_select)) > 8: | |
28 $params.input_hgvs_table_name9 $params.input_hgvs_table9 | |
29 #end if | |
30 </command> | |
31 <inputs> | |
32 <param name="collapse" type="boolean" truevalue="true" falsevalue="false" value="False" label="Collapse stats. If unchecked, column values for zygosity, quality, variant and total depth will have multiple values separated by ';'. If checked, each of these columns will be averaged out amongst input values to report a consensus."/> | |
33 <conditional name="params"> | |
34 <param name="source_select" type="select" label="Number of variant call tables to combine"> | |
35 <option value="2" selected="true">2</option> | |
36 <option value="3">3</option> | |
37 <option value="4">4</option> | |
38 <option value="5">5</option> | |
39 <option value="6">6</option> | |
40 <option value="7">7</option> | |
41 <option value="8">8</option> | |
42 <option value="9">9</option> | |
43 </param> | |
44 <when value="2"> | |
45 <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/> | |
46 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
47 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
48 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
49 </when> | |
50 <when value="3"> | |
51 <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/> | |
52 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
53 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
54 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
55 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
56 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
57 </when> | |
58 <when value="4"> | |
59 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
60 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
61 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
62 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
63 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
64 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
65 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
66 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
67 </when> | |
68 <when value="5"> | |
69 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
70 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
71 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
72 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
73 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
74 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
75 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
76 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
77 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/> | |
78 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/> | |
79 </when> | |
80 <when value="6"> | |
81 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
82 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
83 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
84 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
85 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
86 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
87 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
88 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
89 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/> | |
90 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/> | |
91 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/> | |
92 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/> | |
93 </when> | |
94 <when value="7"> | |
95 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
96 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
97 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
98 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
99 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
100 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
101 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
102 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
103 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/> | |
104 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/> | |
105 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/> | |
106 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/> | |
107 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/> | |
108 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/> | |
109 </when> | |
110 <when value="8"> | |
111 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
112 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
113 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
114 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
115 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
116 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
117 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
118 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
119 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/> | |
120 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/> | |
121 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/> | |
122 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/> | |
123 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/> | |
124 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/> | |
125 <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/> | |
126 <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/> | |
127 </when> | |
128 <when value="9"> | |
129 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/> | |
130 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/> | |
131 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/> | |
132 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/> | |
133 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/> | |
134 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/> | |
135 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/> | |
136 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/> | |
137 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/> | |
138 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/> | |
139 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/> | |
140 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/> | |
141 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/> | |
142 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/> | |
143 <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/> | |
144 <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/> | |
145 <param name="input_hgvs_table_name9" type="text" label="Dataset name #9"/> | |
146 <param format="achri_snp_table" name="input_hgvs_table9" type="data" label="Nineth table"/> | |
147 </when> | |
148 </conditional> | |
149 </inputs> | |
150 <outputs> | |
151 <data format="achri_snp_table" name="output_hgvs_table" type="data" label="HGVS variant table, combining multiple call sets"/> | |
152 </outputs> | |
153 | |
154 <tests> | |
155 </tests> | |
156 | |
157 <help> | |
158 This tool takes multiple annotated HGVS variant tables and outputs a single table with an extra last column describing the list of input tables that reported the variant. | |
159 This may be used to combine multiple variant predictions for the same sample (e.g. a frameshift detection tool and a SNP tool, or two SNP tools using different algorithms). | |
160 It may also be used to highlight the concordance between individuals with similar phenotypes (common genetic cause), or isolate de novo mutations in a child (where trio data is available).</help> | |
161 | |
162 | |
163 </tool> |