Mercurial > repos > greg > gene_family_phylogeny_builder
changeset 4:b78f5b0d0805 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 11 Apr 2017 13:13:53 -0400 |
| parents | 09a1b1b5aa0d |
| children | f73151ec679b |
| files | gene_family_phylogeny_builder.xml |
| diffstat | 1 files changed, 25 insertions(+), 20 deletions(-) [+] |
line wrap: on
line diff
--- a/gene_family_phylogeny_builder.xml Tue Apr 11 13:05:34 2017 -0400 +++ b/gene_family_phylogeny_builder.xml Tue Apr 11 13:13:53 2017 -0400 @@ -19,7 +19,31 @@ #end if python $__tool_directory__/gene_family_phylogeny_builder.py - --orthogroup_aln '$input_aln.extra_files_path' + #if str($input_format) == 'ptalign': + --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path' + --alignment_type 'aln' + --sequence_type 'protein' + #else if str($input_format) == 'ptalignca': + --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path' + --alignment_type 'aln' + --sequence_type $input_format_cond.sequence_type + #else if str($input_format) == 'ptalignfiltered': + --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path' + --alignment_type 'filter' + --sequence_type 'protein' + #else if str($input_format) == 'ptalignfilteredca': + --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path' + --alignment_type 'filter' + --sequence_type $input_format_cond.sequence_type + #else if str($input_format) == 'ptaligntrimmed': + --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path' + --alignment_type 'trim' + --sequence_type 'protein' + #else if str($input_format) == 'ptaligntrimmedca': + --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path' + --alignment_type 'trim' + --sequence_type $input_format_cond.sequence_type + #end if --scaffold '$scaffold.fields.path' --config_dir '$scaffold.fields.path' --method $method @@ -35,25 +59,6 @@ --min_orthogroup_size $min_orthogroup_size --max_orthogroup_size $max_orthogroup_size --num_threads \${GALAXY_SLOTS:-4} - #if str($input_format) == 'ptalign': - --alignment_type 'aln' - --sequence_type 'protein' - #else if str($input_format) == 'ptalignca': - --alignment_type 'aln' - --sequence_type $input_format_cond.sequence_type - #else if str($input_format) == 'ptalignfiltered': - --alignment_type 'filter' - --sequence_type 'protein' - #else if str($input_format) == 'ptalignfilteredca': - --alignment_type 'filter' - --sequence_type $input_format_cond.sequence_type - #else if str($input_format) == 'ptaligntrimmed': - --alignment_type 'trim' - --sequence_type 'protein' - #else if str($input_format) == 'ptaligntrimmedca': - --alignment_type 'trim' - --sequence_type $input_format_cond.sequence_type - #end if --output '$output_pttree' --output_dir '$output_pttree.files_path' ]]>