Mercurial > repos > miller-lab > genome_diversity

annotate draw_variants.xml @ 39:e56023008e36 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Changed revision of package_fisher_0_1_4 to be2fc454d121 Changed revision of package_matplotlib_1_2 to a03ee94316b5
author miller-lab
date Mon, 06 Jul 2015 10:32:24 -0400
parents a631c2f6d913
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
1 <tool id="gd_draw_variants" name="Draw variants" version="1.1.0">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
2 <description>: show positions of SNVs and unsequenced intervals</description>
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
3
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
4 <command interpreter="python">
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
5 #import json
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
6 #import base64
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 24
diff changeset
7 #import zlib
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
8 #if $use_snp.choice == '1'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
9 #set $snp_file = $use_snp.snp_input
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
10 #set $snp_ext = $use_snp.snp_input.ext
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
11 #set $snp_names = $use_snp.snp_input.dataset.metadata.individual_names
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
12 #set $snp_colms = $use_snp.snp_input.dataset.metadata.individual_columns
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
13 #set $snp_dict = dict(zip($snp_names, $snp_colms))
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
14 #set $snp_json = json.dumps($snp_dict, separators=(',',':'))
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
15 #set $snp_comp = zlib.compress($snp_json, 9)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
16 #set $snp_arg = base64.b64encode($snp_comp)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
17 #else
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
18 #set $snp_file = '/dev/null'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
19 #set $snp_ext = ''
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
20 #set $snp_arg = ''
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
21 #end if
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
22 #if $use_cov.choice == '1'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
23 #set $cov_file = $use_cov.cov_input
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
24 #set $cov_ext = $use_cov.cov_input.ext
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
25 #set $cov_names = $use_cov.cov_input.dataset.metadata.individual_names
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
26 #set $cov_colms = $use_cov.cov_input.dataset.metadata.individual_columns
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
27 #set $cov_dict = dict(zip($cov_names, $cov_colms))
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
28 #set $cov_json = json.dumps($cov_dict, separators=(',',':'))
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
29 #set $cov_comp = zlib.compress($cov_json, 9)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
30 #set $cov_arg = base64.b64encode($cov_comp)
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
31 #set $cov_min = $use_cov.min_coverage
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
32 #else
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
33 #set $cov_file = '/dev/null'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
34 #set $cov_ext = ''
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
35 #set $cov_arg = ''
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
36 #set $cov_min = 0
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
37 #end if
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
38 #if $use_indiv.choice == '1'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
39 #set $ind_arg = $use_indiv.indiv_input
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
40 #else
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
41 #set $ind_arg = '/dev/null'
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
42 #end if
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
43 draw_variants.py '$snp_file' '$snp_ext' '$snp_arg' '$ind_arg' '$annotation_input' '$cov_file' '$cov_ext' '$cov_arg' '$cov_min' '$output'
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
44 </command>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
45
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
46 <inputs>
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
47 <conditional name="use_snp">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
48 <param name="choice" type="select" format="integer" label="Include SNP/Genotype dataset">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
49 <option value="1" selected="true">yes</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
50 <option value="0">no</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
51 </param>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
52 <when value="0" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
53 <when value="1">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
54 <param name="snp_input" type="data" format="gd_snp,gd_genotype" label="SNP/Genotype dataset" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
55 </when>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
56 </conditional>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
57 <conditional name="use_cov">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
58 <param name="choice" type="select" format="integer" label="Include Coverage dataset">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
59 <option value="1" selected="true">yes</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
60 <option value="0">no</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
61 </param>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
62 <when value="0" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
63 <when value="1">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
64 <param name="cov_input" type="data" format="gd_snp,gd_genotype" label="Coverage dataset" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
65 <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
66 </when>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
67 </conditional>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
68 <conditional name="use_indiv">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
69 <param name="choice" type="select" label="Compute for">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
70 <option value="0" selected="true">All individuals</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
71 <option value="1">Individuals in a population</option>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
72 </param>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
73 <when value="0" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
74 <when value="1">
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
75 <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
76 </when>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
77 </conditional>
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
78 <param name="annotation_input" type="data" format="interval" label="Annotation dataset" />
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
79 </inputs>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
80
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
81 <outputs>
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
82 <data name="output" format="tiff" />
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
83 </outputs>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
84
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
85 <requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
86 <requirement type="package" version="0.1">gd_c_tools</requirement>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
87 </requirements>
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
88
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
89 <help>
31
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
90 **What it does**
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
91
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
92 The user supplies the following:
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
93
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
94 1. A optional file in gd_genotype or gd_snp format giving the mitochondrial SNPs.
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
95 2. An optional gd_genotype file gives the sequence coverage for each individual at each mitochondrial position.
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
96 3. The minimum depth of sequence coverage. Positions where an individual has less coverage are ignoried.
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
97 4. A set of individuals specified with the "Specify individuals" tool.
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
98 5. A file of annotation for the reference mitochondrial sequence.
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
99
a631c2f6d913 Update to Miller Lab devshed revision 3c4110ffacc3
Richard Burhans <burhans@bx.psu.edu>
parents: 27
diff changeset
100 The program draws a picture indicating the locations of SNPs and the inadequately covered interval.
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
101 </help>
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
102 </tool>