Mercurial > repos > jaredgk > ppp_vcfphase

comparison vcf_phase.xml @ 0:3830d29fca6a draft

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author jaredgk
date Mon, 15 Oct 2018 18:15:47 -0400
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-1:000000000000 0:3830d29fca6a
1 <tool id="vcf_phase" name="Phase VCF" version="1.0.0.1">
2
3 <description>files with BEAGLE or SHAPEIT</description>
4
5 <requirements>
6 <requirement type="package" >pandas</requirement>
7 <requirement type="package" >pysam</requirement>
8 <requirement type="package" >shapeit</requirement>
9 <requirement type="package" >beagle</requirement>
10 </requirements>
11
12 <command><![CDATA[
13 #if $input.is_of_type('vcf_bgzip')
14 ln -fs $input input.vcf.gz &&
15 #end if
16 #if $input.is_of_type('vcf')
17 ln -fs $input input.vcf &&
18 #end if
19 python $__tool_directory__/vcf_phase.py
20 #if $input.is_of_type('vcf_bgzip')
21 --vcf input.vcf.gz
22 #end if
23 #if $input.is_of_type('vcf')
24 --vcf input.vcf
25 #end if
26 #if $model_file
27 --model-file $model_file
28 --model $model
29 #end if
30 --phase-algorithm $phase.phase_algorithm
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 --beagle-path $__tool_data_path__/shared/jars/
39 #if $phase.beagle_iter
40 --beagle-iter $phase.beagle_iter
41 #end if
42 #if $phase.beagle_states
43 --beagle-states $phase.beagle_states
44 #end if
45 #if $phase.beagle_window
46 --beagle-window $phase.beagle_window
47 #end if
48 #if $phase.beagle_overlap
49 --beagle-overlap $phase.beagle_overlap
50 #end if
51 #if $phase.beagle_error
52 --beagle-error $phase.beagle_error
53 #end if
54 #if $phase.beagle_step
55 --beagle-step $phase.beagle_step
56 #end if
57 #if $phase.beagle_nsteps
58 --beagle-nsteps $phase.beagle_nsteps
59 #end if
60 #end if
61 #if $phase.phase_algorithm == 'shapeit'
62 #if $phase.shapeit_burn_iter
63 --shapeit-burn-iter $phase.shapeit_burn_iter
64 #end if
65 #if $phase.shapeit_prune_iter
66 --shapeit-prune-iter $phase.shapeit_prune_iter
67 #end if
68 #if $phase.shapeit_main_iter
69 --shapeit-main-iter $phase.shapeit_main_iter
70 #end if
71 #if $phase.shapeit_states
72 --shapeit-states $phase.shapeit_states
73 #end if
74 #if $phase.shapeit_window
75 --shapeit-window $phase.shapeit_window
76 #end if
77 #end if
78 #if $common.genetic_map
79 --genetic-map $common.genetic_map
80 #end if
81 #if $common.ne
82 --Ne $common.ne
83 #end if
84 #if $common.random_seed
85 --random-seed $common.random_seed
86 #end if
87 #if $common.phase_chr
88 --phase-chr $common.phase_chr
89 #end if
90 #if $common.phase_from_bp
91 --phase-from-bp $common.phase_from_bp
92 #end if
93 #if $common.phase_to_bp
94 --phase-to-bp $common.phase_to_bp
95 #end if
96 --out $output
97 --out-format $out_format
98 ]]></command>
99
100 <inputs>
101
102 <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/>
103
104 <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">
106 <options>
107 <filter type="data_meta" ref="model_file" key="models"/>
108 </options>
109 </param>
110
111 <conditional name="phase">
112 <param name="phase_algorithm" type="select" label="Phase Algorithm" refresh_on_change='True'>
113 <option value="beagle" selected="True" >Beagle</option>
114 <option value="shapeit">SHAPEIT</option>
115 </param>
116 <when value="beagle">
117 <param name="beagle_burn_iter" type="integer" label="Burn-in iterations" optional="True"/>
118 <param name="beagle_iter" type="integer" label="Post burn-in iterations" optional="True"/>
119 <param name="beagle_states" type="integer" label="Model states for genotype estimation" optional="True"/>
120 <param name="beagle_window" type="float" label="Sliding window size (cM)" optional="True"/>
121 <param name="beagle_overlap" type="float" label="Overlap between neighboring sliding windows (cM)" optional="True"/>
122 <param name="beagle_error" type="float" label="HMM allele mismatch probability" optional="True"/>
123 <param name="beagle_step" type="float" label="Step length (cM)" optional="True" help="Used for identifying short IBS segments"/>
124 <param name="beagle_nsteps" type="integer" label="Number of consecutive steps" optional="True" help="Used for identifying long IBS segments"/>
125 </when>
126 <when value="shapeit">
127 <param name="shapeit_burn_iter" type="integer" label="Burn-in iterations" optional="True"/>
128 <param name="shapeit_prune_iter" type="integer" label="Pruning iterations" optional="True"/>
129 <param name="shapeit_main_iter" type="integer" label="Main iterations" optional="True"/>
130 <param name="shapeit_states" type="integer" label="Conditioning states for haplotype estimation" optional="True"/>
131 <param name="shapeit_window" type="float" label="Model window size (Mb)" optional="True"/>
132 </when>
133 </conditional>
134
135 <section name="common" title="Common Parameters" expanded="True">
136 <param name="random_seed" type="integer" label="Seed value" optional="True"/>
137 <param format="text" name="genetic_map" type="data" label="Genetic Map" optional="True"/>
138 <param name="ne" type="integer" label="Effective population size" optional="True"/>
139 <param name="phase_chr" type="text" label="Chromosome to phase" optional="True"/>
140 <param name="phase_from_bp" type="integer" label="Lower bound of sites to include" help="Only usable with a single chromosome" optional="True"/>
141 <param name="phase_to_bp" type="integer" label="Upper bound of sites to include" help="Only usable with a single chromosome" optional="True"/>
142 </section>
143
144 <param name="out_format" type="select" label="Output Format">
145 <option value="vcf">VCF File</option>
146 <option value="vcf.gz" selected="True">bgzipped-VCF File</option>
147 <option value="bcf">BCF File</option>
148 </param>
149
150 </inputs>
151 <outputs>
152
153 <data name="output" format="vcf_bgzip">
154 <change_format>
155 <when input="out_format" value="vcf" format="vcf"/>
156 <when input="out_format" value="bcf" format="bcf"/>
157 </change_format>
158 </data>
159
160 </outputs>
161
162 <help>
163 VCF Phaser Help Text
164 </help>
165
166 </tool>