Mercurial > repos > miller-lab > genome_diversity
comparison add_fst_column.xml @ 27:8997f2ca8c7a
Update to Miller Lab devshed revision bae0d3306d3b
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Mon, 15 Jul 2013 10:47:35 -0400 |
| parents | 248b06e86022 |
| children | a631c2f6d913 |
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| 26:91e835060ad2 | 27:8997f2ca8c7a |
|---|---|
| 1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.2.0"> | 1 <tool id="gd_add_fst_column" name="Per-SNP FSTs" version="1.2.0"> |
| 2 <description>: Compute a fixation index score for each SNP</description> | 2 <description>: Compute a fixation index score for each SNP</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 add_fst_column.py "$input" "$p1_input" "$p2_input" | 5 #import json |
| 6 #import base64 | |
| 7 #import zlib | |
| 8 #set $ind_names = $input.dataset.metadata.individual_names | |
| 9 #set $ind_colms = $input.dataset.metadata.individual_columns | |
| 10 #set $ind_dict = dict(zip($ind_names, $ind_colms)) | |
| 11 #set $ind_json = json.dumps($ind_dict, separators=(',',':')) | |
| 12 #set $ind_comp = zlib.compress($ind_json, 9) | |
| 13 #set $ind_arg = base64.b64encode($ind_comp) | |
| 14 add_fst_column.py '$input' '$p1_input' '$p2_input' | |
| 6 #if $input_type.choice == '0' | 15 #if $input_type.choice == '0' |
| 7 "gd_snp" "$input_type.data_source.choice" | 16 'gd_snp' '$input_type.data_source.choice' |
| 8 #if $input_type.data_source.choice == '0' | 17 #if $input_type.data_source.choice == '0' |
| 9 "$input_type.data_source.min_reads" "$input_type.data_source.min_qual" | 18 '$input_type.data_source.min_reads' '$input_type.data_source.min_qual' |
| 10 #else if $input_type.data_source.choice == '1' | 19 #else if $input_type.data_source.choice == '1' |
| 11 "0" "0" | 20 '0' '0' |
| 12 #end if | 21 #end if |
| 13 #else if $input_type.choice == '1' | 22 #else if $input_type.choice == '1' |
| 14 "gd_genotype" "1" "0" "0" | 23 'gd_genotype' '1' '0' '0' |
| 15 #end if | 24 #end if |
| 16 "$retain" "$discard_fixed" "$biased" "$output" | 25 '$retain' '$discard_fixed' '$biased' '$output' '$ind_arg' |
| 17 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 18 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 19 "$arg" | |
| 20 #end for | |
| 21 </command> | 26 </command> |
| 22 | 27 |
| 23 <inputs> | 28 <inputs> |
| 24 <conditional name="input_type"> | 29 <conditional name="input_type"> |
| 25 <param name="choice" type="select" format="integer" label="Input format"> | 30 <param name="choice" type="select" format="integer" label="Input format"> |