| Previous changeset 0:3830d29fca6a (2018-10-15) Next changeset 2:54c84f7dcb2c (2018-10-17) |
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Commit message:
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modified:
vcf_phase.xml |
| b |
| diff -r 3830d29fca6a -r 15245deda141 vcf_phase.xml --- a/vcf_phase.xml Mon Oct 15 18:15:47 2018 -0400 +++ b/vcf_phase.xml Tue Oct 16 18:03:51 2018 -0400 |
| [ |
| @@ -5,40 +5,44 @@ <requirements> <requirement type="package" >pandas</requirement> <requirement type="package" >pysam</requirement> + <requirement type="package" >beagle</requirement> <requirement type="package" >shapeit</requirement> - <requirement type="package" >beagle</requirement> </requirements> <command><![CDATA[ #if $input.is_of_type('vcf_bgzip') ln -fs $input input.vcf.gz && + ln -fs $input.metadata.tabix_index input.vcf.gz.tbi && #end if #if $input.is_of_type('vcf') ln -fs $input input.vcf && #end if python $__tool_directory__/vcf_phase.py + --phase-algorithm $phase.phase_algorithm + --out $output + --out-format $out_format + #if $input.is_of_type('vcf_bgzip') --vcf input.vcf.gz #end if + #if $input.is_of_type('vcf') --vcf input.vcf #end if + #if $model_file --model-file $model_file --model $model #end if - --phase-algorithm $phase.phase_algorithm - #if $phase.beagle_burn_iter - --beagle-burn-iter $common.beagle_burn_iter - #end if - #if $phase.beagle_burn_iter - --beagle-burn-iter $phase.beagle_burn_iter - #end if + #if $phase.phase_algorithm == 'beagle' --beagle-path $__tool_data_path__/shared/jars/ #if $phase.beagle_iter --beagle-iter $phase.beagle_iter #end if + #if $phase.beagle_burn_iter + --beagle-burn-iter $phase.beagle_burn_iter + #end if #if $phase.beagle_states --beagle-states $phase.beagle_states #end if @@ -58,6 +62,7 @@ --beagle-nsteps $phase.beagle_nsteps #end if #end if + #if $phase.phase_algorithm == 'shapeit' #if $phase.shapeit_burn_iter --shapeit-burn-iter $phase.shapeit_burn_iter @@ -75,26 +80,32 @@ --shapeit-window $phase.shapeit_window #end if #end if + #if $common.genetic_map --genetic-map $common.genetic_map #end if + #if $common.ne --Ne $common.ne #end if + #if $common.random_seed --random-seed $common.random_seed #end if + #if $common.phase_chr --phase-chr $common.phase_chr #end if + #if $common.phase_from_bp --phase-from-bp $common.phase_from_bp #end if + #if $common.phase_to_bp --phase-to-bp $common.phase_to_bp #end if - --out $output - --out-format $out_format + + ]]></command> <inputs> @@ -102,7 +113,7 @@ <param format="vcf,vcf_bgzip" name="input" type="data" label="VCF Input"/> <param format="model" name="model_file" type="data" label="Model Input" optional="True"/> - <param name="model" type="select" label="Select Model" refresh_on_change="True"> + <param name="model" type="select" label="Select Model" refresh_on_change="True" optional="True"> <options> <filter type="data_meta" ref="model_file" key="models"/> </options> |