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 |
| parents | |
| children | 15245deda141 |
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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> |