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comparison specify.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents fdb4240fb565
children 8997f2ca8c7a
comparison
equal deleted inserted replaced
23:66a183c44dd5 24:248b06e86022
1 <tool id="gd_specify" name="Specify Individuals" version="1.0.0"> 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="bash"> 4 <command interpreter="python">
5 echo.bash "$input" "$output" 5 specify.py "$input" "$output"
6 #for $individual in str($individuals).split(',') 6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
7 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual) 7 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
8 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] ) 8 "$individual_arg"
9 #set $arg = '\t'.join([$individual_col, $individual, ''])
10 "$arg"
11 #end for 9 #end for
10 #if str($individuals).strip() != 'None'
11 #for $individual in str($individuals).split(',')
12 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
13 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
14 #set $cb_arg = 'checkbox:%s:%s' % ($individual_col, $individual)
15 "$cb_arg"
16 #end for
17 #end if
18 #if str($string).strip() != ''
19 #set str_arg = 'string:%s' % ( __import__('base64').b64encode( str($string) ) )
20 "$str_arg"
21 #end if
12 </command> 22 </command>
13 23
14 <inputs> 24 <inputs>
15 <param name="input" type="data" format="gd_snp" label="SNP dataset"/> 25 <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP or Genotype dataset"/>
16 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> 26 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
17 <options> 27 <options>
18 <filter type="data_meta" ref="input" key="individual_names" /> 28 <filter type="data_meta" ref="input" key="individual_names" />
19 </options> 29 </options>
20 <validator type="no_options" message="You must select at least one individual."/>
21 </param> 30 </param>
22 <param name="outname" type="text" size="20" label="Label for this collection"> 31 <param name="outname" type="text" size="20" label="Label for this collection">
23 <validator type="empty_field" message="You must enter a label."/> 32 <validator type="empty_field" message="You must enter a label."/>
24 #used to be "Individuals from ${input.hid}" 33 #used to be "Individuals from ${input.hid}"
34 </param>
35 <param name="string" type="text" size="40" label="Individuals to include">
36 <sanitizer>
37 <valid initial="string.printable"/>
38 </sanitizer>
25 </param> 39 </param>
26 </inputs> 40 </inputs>
27 41
28 <outputs> 42 <outputs>
29 <data name="output" format="gd_indivs" label="${outname}" /> 43 <data name="output" format="gd_indivs" label="${outname}" />
39 53
40 <help> 54 <help>
41 55
42 **Dataset formats** 56 **Dataset formats**
43 57
44 The input dataset is in gd_snp_ format; 58 The input dataset is in gd_snp_ or gd_genotype_ format;
45 the output is in gd_indivs_ format. (`Dataset missing?`_) 59 the output is in gd_indivs_ format. (`Dataset missing?`_)
46 60
47 .. _gd_snp: ./static/formatHelp.html#gd_snp 61 .. _gd_snp: ./static/formatHelp.html#gd_snp
62 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
48 .. _gd_indivs: ./static/formatHelp.html#gd_indivs 63 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
49 .. _Dataset missing?: ./static/formatHelp.html 64 .. _Dataset missing?: ./static/formatHelp.html
50 65
51 ----- 66 -----
52 67
53 **What it does** 68 **What it does**
54 69
55 This tool makes a list of selected entities (the sets of four columns 70 This tool makes a list of selected entities, i.e., the sets of four
56 representing individuals or groups) from a gd_snp dataset. It does not copy 71 columns representing individuals or groups from a gd_snp dataset, or
57 the SNP data; it just records which entities should be considered as belonging 72 sets of single columns in a gd_genotype file. It does not copy the
58 to some collection or population. The label you specify is used to name the 73 data; it just records which entities should be considered as belonging
59 output dataset in your history. This list can then be used to instruct other 74 to some collection or population. The label you specify is used to
60 tools to work on just part of the original gd_snp dataset. 75 name the output dataset in your history. This list can then be used
76 to instruct other tools to work on just part of the original gd_snp or
77 gd_genotype dataset. The entities can be specified with the checklist
78 and/or by pasting their names (possibly with extraneous characters, as
79 in a portion of the Newick-format output of the Phylogenetic Tree tool)
80 into the box provided at the bottom of the page.
61 81
62 ----- 82 -----
63 83
64 **Example** 84 **Example**
65 85