Mercurial > repos > miller-lab > genome_diversity
comparison specify.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 |
comparison
equal
deleted
inserted
replaced
| 26:91e835060ad2 | 27:8997f2ca8c7a |
|---|---|
| 1 <tool id="gd_specify" name="Specify Individuals" version="1.1.0"> | 1 <tool id="gd_specify" name="Specify Individuals" version="1.1.0"> |
| 2 <description>: Define a collection of individuals from a gd_snp dataset</description> | 2 <description>: Define a collection of individuals from a gd_snp dataset</description> |
| 3 | 3 |
| 4 <command interpreter="python"> | 4 <command interpreter="python"> |
| 5 specify.py "$input" "$output" | 5 #import json |
| 6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | 6 #import base64 |
| 7 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual) | 7 #import zlib |
| 8 "$individual_arg" | 8 #set $ind_names = $input.dataset.metadata.individual_names |
| 9 #end for | 9 #set $ind_colms = $input.dataset.metadata.individual_columns |
| 10 #if str($individuals).strip() != 'None' | 10 #set $ind_dict = dict(zip($ind_names, $ind_colms)) |
| 11 #for $individual in str($individuals).split(',') | 11 #set $ind_json = json.dumps($ind_dict, separators=(',',':')) |
| 12 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual) | 12 #set $ind_comp = zlib.compress($ind_json, 9) |
| 13 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] ) | 13 #set $ind_arg = base64.b64encode($ind_comp) |
| 14 #set $cb_arg = 'checkbox:%s:%s' % ($individual_col, $individual) | 14 #set $cb_string = str($individuals).strip() |
| 15 "$cb_arg" | 15 #if $cb_string != 'None' |
| 16 #end for | 16 #set $cb_dict = dict.fromkeys($cb_string.split('\t')) |
| 17 #for $cb_name in $cb_dict: | |
| 18 #set $cb_idx = $input.dataset.metadata.individual_names.index($cb_name) | |
| 19 #set $cb_dict[$cb_name] = str($input.dataset.metadata.individual_columns[$cb_idx]) | |
| 20 #end for | |
| 21 #else | |
| 22 #set $cb_dict = dict() | |
| 17 #end if | 23 #end if |
| 18 #if str($string).strip() != '' | 24 #set $cb_json = json.dumps($cb_dict, separators=(',',':')) |
| 19 #set str_arg = 'string:%s' % ( __import__('base64').b64encode( str($string) ) ) | 25 #set $cb_comp = zlib.compress($cb_json, 9) |
| 20 "$str_arg" | 26 #set $cb_arg = base64.b64encode($cb_comp) |
| 21 #end if | 27 #set $str_string = str($string).strip() |
| 28 #set $str_comp = zlib.compress($str_string, 9) | |
| 29 #set $str_arg = base64.b64encode($str_comp) | |
| 30 specify.py '$input' '$output' '$ind_arg' '$cb_arg' '$str_arg' | |
| 22 </command> | 31 </command> |
| 23 | 32 |
| 24 <inputs> | 33 <inputs> |
| 25 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP or Genotype dataset"/> | 34 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP or Genotype dataset"/> |
| 26 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> | 35 <param name="individuals" type="select" display="checkboxes" multiple="true" separator="	" label="Individuals to include"> |
| 27 <options> | 36 <options> |
| 28 <filter type="data_meta" ref="input" key="individual_names" /> | 37 <filter type="data_meta" ref="input" key="individual_names" /> |
| 29 </options> | 38 </options> |
| 30 </param> | 39 </param> |
| 31 <param name="outname" type="text" size="20" label="Label for this collection"> | 40 <param name="outname" type="text" size="20" label="Label for this collection"> |
| 32 <validator type="empty_field" message="You must enter a label."/> | 41 <validator type="empty_field" message="You must enter a label."/> |
| 33 #used to be "Individuals from ${input.hid}" | 42 #used to be "Individuals from ${input.hid}" |
| 34 </param> | 43 </param> |
| 35 <param name="string" type="text" size="40" label="Individuals to include"> | 44 <param name="string" type="text" area="true" size="5x40" label="Individuals to include"> |
| 36 <sanitizer> | 45 <sanitizer> |
| 37 <valid initial="string.printable"/> | 46 <valid initial="string.printable"/> |
| 38 </sanitizer> | 47 </sanitizer> |
| 39 </param> | 48 </param> |
| 40 </inputs> | 49 </inputs> |