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comparison gemini_macros.xml @ 0:66bc68095012 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:56:02 -0500
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-1:000000000000 0:66bc68095012
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="0.18.1">gemini</requirement>
5 <yield />
6 </requirements>
7 </xml>
8
9 <xml name="version_command">
10 <version_command>gemini --version</version_command>
11 </xml>
12
13 <xml name="stdio">
14 <stdio>
15 <exit_code range="1:" />
16 <exit_code range=":-1" />
17 <regex match="Error:" />
18 <regex match="Exception:" />
19 </stdio>
20 </xml>
21
22 <xml name="annotation_dir">
23 <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
24 <options from_data_table="gemini_databases">
25 <filter type="sort_by" column="0" />
26 </options>
27 </param>
28 </xml>
29
30 <xml name="add_header_column">
31 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
32 label="Add a header of column names to the output" help="(--header)"/>
33 </xml>
34
35 <xml name="radius">
36 <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
37 <validator type="in_range" min="0"/>
38 </param>
39 </xml>
40 <xml name="variant_mode">
41 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
42 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
43 </xml>
44
45 <xml name="column_filter">
46 <conditional name="report">
47 <param name="report_selector" type="select" label="Columns to include in the report"
48 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
49 <option value="all" selected="True">all</option>
50 <option value="column_filter">User given columns</option>
51 </param>
52 <when value="all"/>
53 <when value="column_filter">
54 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
55 <option value="gene">gene</option>
56 <option value="chrom">chrom</option>
57 <option value="start">start</option>
58 <option value="end">end</option>
59 <option value="ref">ref</option>
60 <option value="alt">alt</option>
61 <option value="impact">impact</option>
62 <option value="impact_severity">impact_severity</option>
63 <option value="max_aaf_all">alternative allele frequency</option>
64 </param>
65 </when>
66 </conditional>
67 </xml>
68
69 <xml name="filter">
70 <conditional name="filter">
71 <param name="filter_selector" type="select" label="Apply additional constraints"
72 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.">
73 <option value="no">No additional constraints</option>
74 <option value="yes">Apply additional constraints</option>
75 </param>
76 <when value="no"/>
77 <when value="yes">
78 <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)">
79 <expand macro="sanitize_query" />
80 </param>
81 </when>
82 </conditional>
83 </xml>
84
85 <xml name="sanitize_query">
86 <sanitizer invalid_char="">
87 <valid initial="string.printable"/>
88 </sanitizer>
89 </xml>
90
91 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
92 #if str($filter.filter_selector) == 'yes' and $filter.filter:
93 #import pipes
94 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
95 #end if
96 </token>
97
98 <xml name="family">
99 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
100 </xml>
101
102 <xml name="lenient">
103 <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>
104 </xml>
105
106 <xml name="unaffected">
107 <param name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False" label="Report candidates that also impact samples labeled as unaffected." help="(--allow-unaffected)"/>
108 </xml>
109
110 <xml name="min_kindreds">
111 <param name="min_kindreds" type="integer" value="1" label="The min. number of kindreds that must have a candidate variant in a gene" help="default: 1 (--min-kindreds)" />
112 </xml>
113
114 <xml name="min_sequence_depth">
115 <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
116 help="default: 0 (-d)" />
117 </xml>
118
119 <xml name="min_gq">
120 <param name="min_gq" type="integer" value="0" label="the minimum genotype quality required for each sample in a family" help="default: 0 (--min-gq)">
121 <validator type="in_range" min="0"/>
122 </param>
123 </xml>
124
125 <xml name="gt_pl_max">
126 <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" />
127 </xml>
128 <token name="@VERSION@">0.18.1</token>
129
130 <xml name="citations">
131 <citations>
132 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
133 <yield />
134 </citations>
135 </xml>
136
137 <xml name="infile">
138 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
139 <options options_filter_attribute="metadata.gemini_version" >
140 <filter type="add_value" value="@VERSION@" />
141 </options>
142 <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>
143 </param>
144 </xml>
145
146 </macros>