Mercurial > repos > jaredgk > ppp_vcfphase
comparison vcf_phase.xml @ 1:15245deda141 draft
Uploaded
| author | jaredgk |
|---|---|
| date | Tue, 16 Oct 2018 18:03:51 -0400 |
| parents | 3830d29fca6a |
| children |
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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 |