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comparison gemini_macros.xml @ 20:b5207530f991 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:19:47 -0500
parents 27ce3de83007
children
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19:27ce3de83007 20:b5207530f991
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="0.10.0">gemini</requirement>
5 <requirement type="package" version="0.1.3">grabix</requirement>
6 <requirement type="package" version="0.2.6">tabix</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement>
8 <requirement type="package" version="2.19.1">bedtools</requirement>
9 <yield />
10 </requirements>
11 </xml>
12
13 <xml name="version_command">
14 <version_command>gemini --version</version_command>
15 </xml>
16
17 <xml name="stdio">
18 <stdio>
19 <exit_code range="1:" />
20 <exit_code range=":-1" />
21 <regex match="Error:" />
22 <regex match="Exception:" />
23 </stdio>
24 </xml>
25
26 <xml name="annotation_dir">
27 <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
28 <options from_data_table="gemini_databases">
29 <filter type="sort_by" column="0" />
30 <validator type="no_options" message="No annotation database is available" />
31 </options>
32 </param>
33 </xml>
34
35 <xml name="add_header_column">
36 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
37 label="Add a header of column names to the output" help="(--header)"/>
38 </xml>
39
40 <xml name="radius">
41 <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
42 <validator type="in_range" min="0"/>
43 </param>
44 </xml>
45 <xml name="variant_mode">
46 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
47 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
48 </xml>
49
50 <xml name="column_filter">
51 <conditional name="report">
52 <param name="report_selector" type="select" label="Columns to include in the report"
53 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
54 <option value="all" selected="True">all</option>
55 <option value="column_filter">User given columns</option>
56 </param>
57 <when value="all"/>
58 <when value="column_filter">
59 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
60 <option value="gene">gene</option>
61 <option value="chrom">chrom</option>
62 <option value="start">start</option>
63 <option value="end">end</option>
64 <option value="ref">ref</option>
65 <option value="alt">alt</option>
66 <option value="impact">impact</option>
67 <option value="impact_severity">impact_severity</option>
68 </param>
69 </when>
70 </conditional>
71 </xml>
72
73 <xml name="filter">
74 <conditional name="filter">
75 <param name="filter_selector" type="select" label="Apply additional constraints"
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.">
77 <option value="no">No additional constraints</option>
78 <option value="yes">Apply additional constraints</option>
79 </param>
80 <when value="no"/>
81 <when value="yes">
82 <param name="filter" type="text" 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)">
83 <expand macro="sanitize_query" />
84 </param>
85 </when>
86 </conditional>
87 </xml>
88
89 <xml name="sanitize_query">
90 <sanitizer invalid_char="">
91 <valid initial="string.printable"/>
92 </sanitizer>
93 </xml>
94
95 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
96 #if str($filter.filter_selector) == 'yes' and $filter.filter:
97 #import pipes
98 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
99 #end if
100 </token>
101
102 <xml name="min_sequence_depth">
103 <param name="d" type="integer" value="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
104 help="default: 0 (-d)">
105 <validator type="in_range" min="0"/>
106 </param>
107 </xml>
108
109 <token name="@VERSION@">0.10.1</token>
110
111 <token name="@CITATION@">------
112
113 **Citation**
114
115 If you use GEMINI in your research, please cite the following manuscript:
116
117 </token>
118 <xml name="citations">
119 <citations>
120 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
121 <yield />
122 </citations>
123 </xml>
124
125 <xml name="infile">
126 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
127 <options options_filter_attribute="metadata.gemini_version" >
128 <filter type="add_value" value="@VERSION@" />
129 </options>
130 <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>
131 </param>
132 </xml>
133
134 </macros>