Mercurial > repos > bobbledavidson > beagle4_0
comparison beagle4.xml @ 2:e7e5432588ea draft
Beagle4 xml wrapper uploaded
author | bobbledavidson |
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date | Wed, 08 Jul 2015 10:19:11 -0400 |
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children | 9e8de4ce2a3c |
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1:c36b11eab590 | 2:e7e5432588ea |
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1 <tool id="Beagle" name="Beagle4.0" > | |
2 <description>Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.</description> | |
3 <requirements> | |
4 <requirement type="package" version="4.0">Beagle</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 | |
8 #if int($useref.refSelect)==0 | |
9 beagle4.py --jar $__tool_directory__/beagle.r1399.jar --gtgl $gtORgl.gtORglSelect --gfile $gtORgl.gtgl --phase-its $phaseits --impute-its $imputeits --out $output | |
10 #else | |
11 beagle4.py --jar $__tool_directory__/beagle.r1399.jar --gtgl $gtORgl.gtORglSelect --gfile $gtORgl.gtgl --ref $useref.ref --phase-its $phaseits --impute-its $imputeits --out $output | |
12 #end if | |
13 | |
14 | |
15 </command> | |
16 | |
17 <inputs> | |
18 | |
19 <conditional name="useref"> | |
20 | |
21 <param name="refSelect" type="select" label="Select to use a reference or to estimate phasing"> | |
22 <option value="1" selected="true">Reference</option> | |
23 <option value="0" >Estimate</option> | |
24 </param> | |
25 | |
26 <when value="1"> | |
27 <param format="vcf" name="ref" type="data" label="Reference file" help="ref=[file] specifies a reference VCF file containing additional samples and phased genotypes for each marker. See also the impute parameter." /> | |
28 </when> | |
29 </conditional> | |
30 | |
31 <conditional name="gtORgl"> | |
32 <param name="gtORglSelect" type="select" label="Select genotype or genotype likelihood input file" help="Either file option requires VCF format"> | |
33 <option value="gt" selected="true">Genotype</option> | |
34 <option value="gl">Genotype Likelihood</option> | |
35 </param> | |
36 <when value="gt"> | |
37 <param format="vcf" name="gtgl" type="data" label="GT file" help="gt=[file] specifies a VCF file containing a GT (genotype) format field for each marker."/> | |
38 </when> | |
39 <when value="gl"> | |
40 <param format="vcf" name="gtgl" type="data" label="GL file" help="gl=[file] specifies a VCF file containing a GL or PL (genotype likelihood) format field for each marker. If both GL and PL format fields are present for a sample, the GL format will be used. See also the maxlr parameter." /> | |
41 </when> | |
42 </conditional> | |
43 | |
44 <param name="imputeits" type="integer" size="3" value="5" label="Impute-ITS (iterations for impute step: default=5)" help="" /> | |
45 <param name="phaseits" type="integer" size="3" value="5" label="Phase-ITS (iterations for phase step: default=5)" /> | |
46 | |
47 </inputs> | |
48 | |
49 <outputs> | |
50 <data format="vcf" name="output" label="Output from Beagle" /> | |
51 | |
52 </outputs> | |
53 | |
54 | |
55 <help> | |
56 | |
57 </help> | |
58 | |
59 | |
60 | |
61 </tool> | |
62 | |
63 | |
64 | |
65 | |
66 | |
67 | |
68 |