Mercurial > repos > miller-lab > genome_diversity
comparison prepare_population_structure.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_prepare_population_structure" name="Prepare Input" version="1.1.0"> | 1 <tool id="gd_prepare_population_structure" name="Prepare Input" version="1.2.0"> |
| 2 <description>: Filter and convert to the format needed for these tools</description> | 2 <description>: Filter and convert to the format needed for these tools</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 prepare_population_structure.py "$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 prepare_population_structure.py '$input' | |
| 6 #if $input_type.choice == '0' | 15 #if $input_type.choice == '0' |
| 7 "gd_snp" "$input_type.min_reads" "$input_type.min_qual" | 16 'gd_snp' '$input_type.min_reads' '$input_type.min_qual' |
| 8 #else if $input_type.choice == '1' | 17 #else if $input_type.choice == '1' |
| 9 "gd_genotype" "0" "0" | 18 'gd_genotype' '0' '0' |
| 10 #end if | 19 #end if |
| 11 "$min_spacing" "$output" "$output.files_path" | 20 '0' '$output' '$output.files_path' '$ind_arg' |
| 12 #if $individuals.choice == '0' | 21 #if $individuals.choice == '0' |
| 13 "all_individuals" | 22 'all_individuals' |
| 14 #else if $individuals.choice == '1' | 23 #else if $individuals.choice == '1' |
| 15 #for $population in $individuals.populations | 24 #for $population in $individuals.populations |
| 16 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) | 25 #set $pop_arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) |
| 17 "$pop_arg" | 26 '$pop_arg' |
| 18 #end for | 27 #end for |
| 19 #end if | 28 #end if |
| 20 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | |
| 21 #set $arg = 'individual:%s:%s' % ($individual_col, $individual) | |
| 22 "$arg" | |
| 23 #end for | |
| 24 </command> | 29 </command> |
| 25 | 30 |
| 26 <inputs> | 31 <inputs> |
| 27 <conditional name="input_type"> | 32 <conditional name="input_type"> |
| 28 <param name="choice" type="select" format="integer" label="Input format"> | 33 <param name="choice" type="select" format="integer" label="Input format"> |
| 50 <param name="p_input" type="data" format="gd_indivs" label="Individuals" /> | 55 <param name="p_input" type="data" format="gd_indivs" label="Individuals" /> |
| 51 </repeat> | 56 </repeat> |
| 52 </when> | 57 </when> |
| 53 </conditional> | 58 </conditional> |
| 54 | 59 |
| 60 <!-- | |
| 55 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" /> | 61 <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs" /> |
| 62 "$min_spacing" "$output" "$output.files_path" | |
| 63 --> | |
| 56 </inputs> | 64 </inputs> |
| 57 | 65 |
| 58 <outputs> | 66 <outputs> |
| 59 <data name="output" format="gd_ped"> | 67 <data name="output" format="gd_ped"> |
| 60 <actions> | 68 <actions> |