Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 22:bacaa8a6e45d draft
Uploaded
| author | greg |
|---|---|
| date | Sat, 07 Jan 2017 09:58:17 -0500 |
| parents | 86a469a50fc4 |
| children | 48479c94a6f3 |
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| 21:86a469a50fc4 | 22:bacaa8a6e45d |
|---|---|
| 31 #set num_orthogroup_fna = $len([f for f in $os.listdir($input_extra_files_path) if f.endswith('.fna')]) | 31 #set num_orthogroup_fna = $len([f for f in $os.listdir($input_extra_files_path) if f.endswith('.fna')]) |
| 32 | 32 |
| 33 #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') | 33 #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') |
| 34 #set dest_fasta_dir = $output_fasta.extra_files_path | 34 #set dest_fasta_dir = $output_fasta.extra_files_path |
| 35 | 35 |
| 36 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments': | 36 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes': |
| 37 #set generate_output_aln = True | 37 #set generate_output_aln = True |
| 38 #set src_aln_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_aln') | 38 #set src_aln_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_aln') |
| 39 #set dest_aln_dir = $output_aln.extra_files_path | 39 #set dest_aln_dir = $output_aln.extra_files_path |
| 40 mkdir -p $dest_aln_dir && | 40 mkdir -p $dest_aln_dir && |
| 41 #else: | 41 #else: |
| 275 </conditional> | 275 </conditional> |
| 276 </inputs> | 276 </inputs> |
| 277 <outputs> | 277 <outputs> |
| 278 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/> | 278 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/> |
| 279 <data name="output_aln" format="txt" label="Sequence alignments and corresponding phylogenies using PASTA on ${on_string}"> | 279 <data name="output_aln" format="txt" label="Sequence alignments and corresponding phylogenies using PASTA on ${on_string}"> |
| 280 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option'] == 'pasta_alignments'</filter> | 280 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter> |
| 281 </data> | 281 </data> |
| 282 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}"> | 282 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}"> |
| 283 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter> | 283 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter> |
| 284 </data> | 284 </data> |
| 285 </outputs> | 285 </outputs> |