annotate gemini_macros.xml @ 1:d3c4d0208bb2 draft

Uploaded
author iuc
date Wed, 27 Aug 2014 02:26:19 -0400
parents 720cbfb4190d
children 93bb0cfacefb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
1 <macros>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
2 <xml name="requirements">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
3 <requirements>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
4 <requirement type="package" version="0.10.0">gemini</requirement>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
5 <requirement type="package" version="0.1.3">grabix</requirement>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
6 <requirement type="package" version="0.2.6">tabix</requirement>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
7 <requirement type="package" version="0.1.19">samtools</requirement>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
8 <requirement type="package" version="2.19.1">bedtools</requirement>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
9 <yield />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
10 </requirements>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
11 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
12
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
13 <xml name="version_command">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
14 <version_command>gemini --version</version_command>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
15 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
16
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
17 <xml name="stdio">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
18 <stdio>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
19 <exit_code range="1:" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
20 <exit_code range=":-1" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
21 <regex match="Error:" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
22 <regex match="Exception:" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
23 </stdio>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
24 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
25
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
26 <xml name="annotation_dir">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
27 <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
28 <options from_data_table="gemini_databases">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
29 <filter type="sort_by" column="0" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
30 <validator type="no_options" message="No annotation database is available" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
31 </options>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
32 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
33 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
34
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
35 <xml name="add_header_column">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
36 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
37 label="Add a header of column names to the output" help="(--header)"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
38 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
39
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
40 <xml name="radius">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
41 <param name="radius" type="integer" value="3" size="5" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
42 <validator type="in_range" min="0"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
43 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
44 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
45 <xml name="variant_mode">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
46 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
47 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
48 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
49
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
50 <xml name="column_filter">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
51 <conditional name="report">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
52 <param name="report_selector" type="select" label="Columns to include in the report"
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
53 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
54 <option value="all" selected="True">all</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
55 <option value="column_filter">User given columns</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
56 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
57 <when value="all"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
58 <when value="column_filter">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
59 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
60 <option value="gene">gene</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
61 <option value="chrom">chrom</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
62 <option value="start">start</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
63 <option value="end">end</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
64 <option value="ref">ref</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
65 <option value="alt">alt</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
66 <option value="impact">impact</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
67 <option value="impact_severity">impact_severity</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
68 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
69 </when>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
70 </conditional>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
71 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
72
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
73 <xml name="filter">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
74 <conditional name="filter">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
75 <param name="filter_selector" type="select" label="Apply additional constraints"
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
76 help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
77 <option value="no">No additional constraints</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
78 <option value="yes">Apply additional constraints</option>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
79 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
80 <when value="no"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
81 <when value="yes">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
82 <param name="filter" type="text" size="20" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
83 <expand macro="sanitize_query" />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
84 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
85 </when>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
86 </conditional>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
87 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
88
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
89 <xml name="sanitize_query">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
90 <sanitizer invalid_char="">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
91 <valid initial="string.printable">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
92 </valid>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
93 </sanitizer>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
94 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
95
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
96 <xml name="min_sequence_depth">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
97 <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample"
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
98 help="default: 0 (-d)">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
99 <validator type="in_range" min="0"/>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
100 </param>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
101 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
102
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
103 <token name="@VERSION@">0.10.0</token>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
104
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
105 <token name="@CITATION@">------
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
106
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
107 **Citation**
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
108
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
109 If you use GEMINI in your research, please cite the following manuscript:
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
110
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
111 </token>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
112 <xml name="citations">
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
113 <citations>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
114 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
115 <yield />
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
116 </citations>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
117 </xml>
720cbfb4190d Imported from capsule None
iuc
parents:
diff changeset
118 </macros>