Mercurial > repos > jaredgk > ppp_vcfphase

comparison vcf_phase.xml @ 1:15245deda141 draft

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author jaredgk
date Tue, 16 Oct 2018 18:03:51 -0400
parents 3830d29fca6a
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0:3830d29fca6a 1:15245deda141
3 <description>files with BEAGLE or SHAPEIT</description> 3 <description>files with BEAGLE or SHAPEIT</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" >pandas</requirement> 6 <requirement type="package" >pandas</requirement>
7 <requirement type="package" >pysam</requirement> 7 <requirement type="package" >pysam</requirement>
8 <requirement type="package" >beagle</requirement>
8 <requirement type="package" >shapeit</requirement> 9 <requirement type="package" >shapeit</requirement>
9 <requirement type="package" >beagle</requirement>
10 </requirements> 10 </requirements>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 #if $input.is_of_type('vcf_bgzip') 13 #if $input.is_of_type('vcf_bgzip')
14 ln -fs $input input.vcf.gz && 14 ln -fs $input input.vcf.gz &&
15 ln -fs $input.metadata.tabix_index input.vcf.gz.tbi &&
15 #end if 16 #end if
16 #if $input.is_of_type('vcf') 17 #if $input.is_of_type('vcf')
17 ln -fs $input input.vcf && 18 ln -fs $input input.vcf &&
18 #end if 19 #end if
19 python $__tool_directory__/vcf_phase.py 20 python $__tool_directory__/vcf_phase.py
21 --phase-algorithm $phase.phase_algorithm
22 --out $output
23 --out-format $out_format
24
20 #if $input.is_of_type('vcf_bgzip') 25 #if $input.is_of_type('vcf_bgzip')
21 --vcf input.vcf.gz 26 --vcf input.vcf.gz
22 #end if 27 #end if
28
23 #if $input.is_of_type('vcf') 29 #if $input.is_of_type('vcf')
24 --vcf input.vcf 30 --vcf input.vcf
25 #end if 31 #end if
32
26 #if $model_file 33 #if $model_file
27 --model-file $model_file 34 --model-file $model_file
28 --model $model 35 --model $model
29 #end if 36 #end if
30 --phase-algorithm $phase.phase_algorithm 37
31 #if $phase.beagle_burn_iter
32 --beagle-burn-iter $common.beagle_burn_iter
33 #end if
34 #if $phase.beagle_burn_iter
35 --beagle-burn-iter $phase.beagle_burn_iter
36 #end if
37 #if $phase.phase_algorithm == 'beagle' 38 #if $phase.phase_algorithm == 'beagle'
38 --beagle-path $__tool_data_path__/shared/jars/ 39 --beagle-path $__tool_data_path__/shared/jars/
39 #if $phase.beagle_iter 40 #if $phase.beagle_iter
40 --beagle-iter $phase.beagle_iter 41 --beagle-iter $phase.beagle_iter
42 #end if
43 #if $phase.beagle_burn_iter
44 --beagle-burn-iter $phase.beagle_burn_iter
41 #end if 45 #end if
42 #if $phase.beagle_states 46 #if $phase.beagle_states
43 --beagle-states $phase.beagle_states 47 --beagle-states $phase.beagle_states
44 #end if 48 #end if
45 #if $phase.beagle_window 49 #if $phase.beagle_window
56 #end if 60 #end if
57 #if $phase.beagle_nsteps 61 #if $phase.beagle_nsteps
58 --beagle-nsteps $phase.beagle_nsteps 62 --beagle-nsteps $phase.beagle_nsteps
59 #end if 63 #end if
60 #end if 64 #end if
65
61 #if $phase.phase_algorithm == 'shapeit' 66 #if $phase.phase_algorithm == 'shapeit'
62 #if $phase.shapeit_burn_iter 67 #if $phase.shapeit_burn_iter
63 --shapeit-burn-iter $phase.shapeit_burn_iter 68 --shapeit-burn-iter $phase.shapeit_burn_iter
64 #end if 69 #end if
65 #if $phase.shapeit_prune_iter 70 #if $phase.shapeit_prune_iter
73 #end if 78 #end if
74 #if $phase.shapeit_window 79 #if $phase.shapeit_window
75 --shapeit-window $phase.shapeit_window 80 --shapeit-window $phase.shapeit_window
76 #end if 81 #end if
77 #end if 82 #end if
83
78 #if $common.genetic_map 84 #if $common.genetic_map
79 --genetic-map $common.genetic_map 85 --genetic-map $common.genetic_map
80 #end if 86 #end if
87
81 #if $common.ne 88 #if $common.ne
82 --Ne $common.ne 89 --Ne $common.ne
83 #end if 90 #end if
91
84 #if $common.random_seed 92 #if $common.random_seed
85 --random-seed $common.random_seed 93 --random-seed $common.random_seed
86 #end if 94 #end if
95
87 #if $common.phase_chr 96 #if $common.phase_chr
88 --phase-chr $common.phase_chr 97 --phase-chr $common.phase_chr
89 #end if 98 #end if
99
90 #if $common.phase_from_bp 100 #if $common.phase_from_bp
91 --phase-from-bp $common.phase_from_bp 101 --phase-from-bp $common.phase_from_bp
92 #end if 102 #end if
103
93 #if $common.phase_to_bp 104 #if $common.phase_to_bp
94 --phase-to-bp $common.phase_to_bp 105 --phase-to-bp $common.phase_to_bp
95 #end if 106 #end if
96 --out $output 107
97 --out-format $out_format 108
98 ]]></command> 109 ]]></command>
99 110
100 <inputs> 111 <inputs>
101 112
102 <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/> 113 <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/>
103 114
104 <param format="model" name="model_file" type="data" label="Model Input" optional="True"/> 115 <param format="model" name="model_file" type="data" label="Model Input" optional="True"/>
105 <param name="model" type="select" label="Select Model" refresh_on_change="True"> 116 <param name="model" type="select" label="Select Model" refresh_on_change="True" optional="True">
106 <options> 117 <options>
107 <filter type="data_meta" ref="model_file" key="models"/> 118 <filter type="data_meta" ref="model_file" key="models"/>
108 </options> 119 </options>
109 </param> 120 </param>
110 121