Mercurial > repos > greg > gene_family_aligner
changeset 12:19529df59e9d draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 10 Apr 2017 14:43:28 -0400 |
| parents | a2b29eb5459d |
| children | d7e6201b8d81 |
| files | gene_family_aligner.xml |
| diffstat | 1 files changed, 44 insertions(+), 54 deletions(-) [+] |
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--- a/gene_family_aligner.xml Mon Apr 10 13:49:04 2017 -0400 +++ b/gene_family_aligner.xml Mon Apr 10 14:43:28 2017 -0400 @@ -10,6 +10,13 @@ #set input_format = $input_format_cond.input_format #set alignment_method_cond = $input_format_cond.alignment_method_cond #set alignment_method = $alignment_method_cond.alignment_method + #if str($input_format_cond.input_format) == 'ptortho': + #set output_codon_alignments == False + #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no': + #set output_codon_alignments == False + #else: + #set output_codon_alignments == True + #end if python $__tool_directory__/gene_family_aligner.py --alignment_method $alignment_method @@ -27,55 +34,44 @@ --codon_alignments 'true' #end if #end if - #if str($options_type_cond.options_type) == 'advanced': - #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond - #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences - #if str($remove_gappy_sequences) == 'yes': - #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond - #set trim_type = $trim_type_cond.trim_type - #if str($trim_type) == 'gap_trimming': - --gap_trimming $trim_type_cond.gap_trimming + #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences + #if str($remove_gappy_sequences) == 'yes': + #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond + #set trim_type = $trim_type_cond.trim_type + #if str($trim_type) == 'gap_trimming': + --gap_trimming $trim_type_cond.gap_trimming + #else: + ## str($trim_type) == 'automated_trimming' + --automated_trimming 'true' + #end if + #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond + #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps + #if str($remove_sequences_with_gaps) == 'yes': + --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of + --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment + #if $output_codon_alignments: + --output '$output_aln_filtered_ca' + --output_dir '$output_aln_filtered_ca.files_path' #else: - ## str($trim_type) == 'automated_trimming' - --automated_trimming 'true' - #end if - #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond - #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps - #if str($remove_sequences_with_gaps) == 'yes': - --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of - --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment - #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): - --output '$output_aln_filtered' - --output_dir '$output_aln_filtered.files_path' - #else: - --output '$output_aln_filtered_ca' - --output_dir '$output_aln_filtered_ca.files_path' - #end if - #else: - #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): - --output '$output_aln_trimmed' - --output_dir '$output_aln_trimmed.files_path' - #else: - --output '$output_aln_trimmed_ca' - --output_dir '$output_aln_trimmed_ca.files_path' - #end if + --output '$output_aln_filtered' + --output_dir '$output_aln_filtered.files_path' #end if #else: - #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): - --output '$output_aln' - --output_dir '$output_aln.files_path' + #if $output_codon_alignments: + --output '$output_aln_trimmed_ca' + --output_dir '$output_aln_trimmed_ca.files_path' #else: - --output '$output_aln_ca' - --output_dir '$output_aln_ca.files_path' + --output '$output_aln_trimmed' + --output_dir '$output_aln_trimmed.files_path' #end if #end if - #esle: - #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): + #else: + #if $output_codon_alignments: + --output '$output_aln_ca' + --output_dir '$output_aln_ca.files_path' + #else: --output '$output_aln' --output_dir '$output_aln.files_path' - #else: - --output '$output_aln_ca' - --output_dir '$output_aln_ca.files_path' #end if #end if ]]> @@ -96,32 +92,26 @@ <expand macro="param_codon_alignments" /> </when> </conditional> - <conditional name="options_type_cond"> - <expand macro="param_options_type" /> - <when value="basic" /> - <when value="advanced"> - <expand macro="cond_remove_gappy_sequences" /> - </when> - </conditional> + <expand macro="cond_remove_gappy_sequences" /> </inputs> <outputs> <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> </data> <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> </data> <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> </data> <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> </data> <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> </data> <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}"> - <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> + <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> </data> </outputs> <tests>