#set input_dir = 'input_dir'
#set tree_inference = $tree_inference_cond.tree_inference
#if str($tree_inference) == 'raxml':
    #set scaffold = $tree_inference_cond.scaffold
    #set method = $tree_inference_cond.method
    #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
    #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
    #if str($rooting_order_file) == 'yes':
        #set rooting_order = $rooting_order_file_cond.rooting_order
    #end if
    #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
#end if
mkdir $input_dir &&
#for $i in $input:
    #set filename = $i.file_name
    #set name = $i.name
    ln -s $filename $input_dir/$name &&
#end for
GeneFamilyPhylogenyBuilder
--orthogroup_aln '$input_dir'
--tree_inference $tree_inference
#if str($tree_inference) == 'raxml':
    --scaffold '$scaffold.fields.path'
    --config_dir '$scaffold.fields.path'
    --method $method
    #if str($rooting_order_file) == 'yes':
        --rooting_order '$rooting_order'
        ## No else block needed here because the default rooting_order
        ## configuration will be used if the --rooting_order flag is missing.
    #end if
    --bootstrap_replicates $bootstrap_replicates
#end if
--min_orthogroup_size $min_orthogroup_size
--max_orthogroup_size $max_orthogroup_size
--num_threads \${GALAXY_SLOTS:-4}
&>gene_family_phylogeny_builder_log.txt;
if [[ $? -ne 0 ]]; then
    find geneFamilyPhylogenies_dir -type d -maxdepth 1 -exec cp gene_family_phylogeny_builder_log.txt {} \;
    exit 1;
fi