Mercurial > repos > dereeper > phyml
changeset 5:c3a69ba72099 draft
Uploaded
| author | dcorreia |
|---|---|
| date | Wed, 04 May 2016 05:41:57 -0400 |
| parents | 95a7626b95ed |
| children | 67555e761895 |
| files | phyml.xml |
| diffstat | 1 files changed, 21 insertions(+), 20 deletions(-) [+] |
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--- a/phyml.xml Mon May 02 07:30:03 2016 -0400 +++ b/phyml.xml Wed May 04 05:41:57 2016 -0400 @@ -17,38 +17,39 @@ ln -sf $input input_tmp; phyml --input input_tmp - $phylip_format - --datatype $seq.type_of_seq - --multiple $nb_data_set + ${phylip_format} + --datatype ${seq.type_of_seq} + --multiple ${nb_data_set} - #if int($support_condition.branchSupport.value) in [0,-1,-2,-4,-5]: - --bootstrap $support_condition.branchSupport + #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']): + --bootstrap ${support_condition.branchSupport} #else: - --bootstrap $support_condition.branchSupport.replicate + --bootstrap ${support_condition.branchSupport.replicate} #end if - #if $seq.type_of_seq == "nt": - -t $seq.tstv + #if ($seq.type_of_seq == "nt"): + -t ${seq.tstv} #end if - --model $seq.model - -f $equi_freq - --pinv $prop_invar + --model ${seq.model} + -f ${equi_freq} + --pinv ${prop_invar} - --nclasses $nbSubstCat - #if $nbSubstCat != "1": - --alpha $gamma + --nclasses ${nbSubstCat} + + #if (str($nbSubstCat) != "1"): + --alpha ${gamma} #end if - --search $move - -o $optimisationTopology + --search ${move} + -o ${optimisationTopology} - #if $usetree.inputTree == "true" : - --inputtree $inputTree.userInputTree + #if ($usetree.inputTree == "true"): + --inputtree ${inputTree.userInputTree} #end if - #if $numStartSeed != "0": - --r_seed $numStartSeed + #if ($numStartSeed != "0"): + --r_seed ${numStartSeed} #end if --no_memory_check