Mercurial > repos > miller-lab > genome_diversity
diff add_fst_column.xml @ 27:8997f2ca8c7a
Update to Miller Lab devshed revision bae0d3306d3b
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Mon, 15 Jul 2013 10:47:35 -0400 |
parents | 248b06e86022 |
children | a631c2f6d913 |
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--- a/add_fst_column.xml Mon Jun 03 12:29:29 2013 -0400 +++ b/add_fst_column.xml Mon Jul 15 10:47:35 2013 -0400 @@ -2,22 +2,27 @@ <description>: Compute a fixation index score for each SNP</description> <command interpreter="python"> - add_fst_column.py "$input" "$p1_input" "$p2_input" + #import json + #import base64 + #import zlib + #set $ind_names = $input.dataset.metadata.individual_names + #set $ind_colms = $input.dataset.metadata.individual_columns + #set $ind_dict = dict(zip($ind_names, $ind_colms)) + #set $ind_json = json.dumps($ind_dict, separators=(',',':')) + #set $ind_comp = zlib.compress($ind_json, 9) + #set $ind_arg = base64.b64encode($ind_comp) + add_fst_column.py '$input' '$p1_input' '$p2_input' #if $input_type.choice == '0' - "gd_snp" "$input_type.data_source.choice" + 'gd_snp' '$input_type.data_source.choice' #if $input_type.data_source.choice == '0' - "$input_type.data_source.min_reads" "$input_type.data_source.min_qual" + '$input_type.data_source.min_reads' '$input_type.data_source.min_qual' #else if $input_type.data_source.choice == '1' - "0" "0" + '0' '0' #end if #else if $input_type.choice == '1' - "gd_genotype" "1" "0" "0" + 'gd_genotype' '1' '0' '0' #end if - "$retain" "$discard_fixed" "$biased" "$output" - #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) - #set $arg = '%s:%s' % ($individual_col, $individual) - "$arg" - #end for + '$retain' '$discard_fixed' '$biased' '$output' '$ind_arg' </command> <inputs>