Mercurial > repos > iuc > gemini_de_novo

annotate gemini_macros.xml @ 3:d5b01cc263be draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
author iuc
date Wed, 17 Oct 2018 13:28:19 -0400
parents 4aabe53ecfe0
children 9db3e299b1c8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
1 <macros>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
2 <xml name="requirements">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
3 <requirements>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
4 <requirement type="package" version="0.18.1">gemini</requirement>
1
8850488002dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 7867095d83e5d0e0f923de7e9720d59df0034817
iuc
parents: 0
diff changeset
5 <requirement type="package" version="0.2.6">tabix</requirement>
2
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
6 <!-- for conda useage -->
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
7 <!--requirement type="package" version="1.3.1">htslib</requirement-->
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
8 <yield />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
9 </requirements>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
10 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
11
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
12 <xml name="version_command">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
13 <version_command>gemini --version</version_command>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
14 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
15
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
16 <xml name="stdio">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
17 <stdio>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
18 <exit_code range="1:" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
19 <exit_code range=":-1" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
20 <regex match="Error:" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
21 <regex match="Exception:" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
22 </stdio>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
23 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
24
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
25 <xml name="annotation_dir">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
26 <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
27 <options from_data_table="gemini_databases">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
28 <filter type="sort_by" column="0" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
29 </options>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
30 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
31 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
32
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
33 <xml name="add_header_column">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
34 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
35 label="Add a header of column names to the output" help="(--header)"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
36 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
37
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
38 <xml name="radius">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
39 <param name="radius" type="integer" value="3" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
40 <validator type="in_range" min="0"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
41 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
42 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
43 <xml name="variant_mode">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
44 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
45 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
46 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
47
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
48 <xml name="column_filter">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
49 <conditional name="report">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
50 <param name="report_selector" type="select" label="Columns to include in the report"
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
51 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
52 <option value="all" selected="True">all</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
53 <option value="column_filter">User given columns</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
54 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
55 <when value="all"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
56 <when value="column_filter">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
57 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
58 <option value="gene">gene</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
59 <option value="chrom">chrom</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
60 <option value="start">start</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
61 <option value="end">end</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
62 <option value="ref">ref</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
63 <option value="alt">alt</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
64 <option value="impact">impact</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
65 <option value="impact_severity">impact_severity</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
66 <option value="max_aaf_all">alternative allele frequency</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
67 </param>
2
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
68 <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/>
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
69 </when>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
70 </conditional>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
71 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
72
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
73 <xml name="filter">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
74 <conditional name="filter">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
75 <param name="filter_selector" type="select" label="Apply additional constraints"
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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.">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
77 <option value="no">No additional constraints</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
78 <option value="yes">Apply additional constraints</option>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
79 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
80 <when value="no"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
81 <when value="yes">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
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)">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
83 <expand macro="sanitize_query" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
84 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
85 </when>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
86 </conditional>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
87 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
88
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
89 <xml name="sanitize_query">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
90 <sanitizer invalid_char="">
3
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
91 <valid initial="string.printable">
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
92 <remove value="&apos;" />
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
93 </valid>
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
94 <mapping initial="none">
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
95 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
96 </mapping>
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
97 </sanitizer>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
98 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
99
3
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
100 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
101 #set $sql_expr = str($multiline_sql_expr).strip()
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
102 #if str($sql_expr):
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
103 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
104 #set $sql_expr = $sql_expr.replace('\r', '\n')
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
105 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
106 $cmdln_param '$sql_expr'
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
107 #end if
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
108 </token>
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
109
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
110 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
111 #if str($filter.filter_selector) == 'yes' and $filter.filter:
3
d5b01cc263be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
iuc
parents: 2
diff changeset
112 --filter '${ str( $filter.filter ) }'
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
113 #end if
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
114 </token>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
115
2
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
116 <token name="@COLUMN_SELECT@">
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
117 #if $report.report_selector != 'all':
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
118 --columns "${report.columns}
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
119 #if str($report.extra_cols).strip()
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
120 #echo ','+','.join(str($report.extra_cols).split())
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
121 #end if
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
122 "
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
123 #end if
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
124 </token>
4aabe53ecfe0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
125
0
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
126 <xml name="family">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
127 <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
128 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
129
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
130 <xml name="lenient">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
131 <param name="lenient" type="boolean" truevalue="--lenient" falsevalue="" checked="False" label="Loosen the restrictions on family structure"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
132 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
133
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
134 <xml name="unaffected">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
135 <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)"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
136 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
137
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
138 <xml name="min_kindreds">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
139 <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)" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
140 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
141
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
142 <xml name="min_sequence_depth">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
143 <param name="d" type="integer" value="0" min="0" label="The minimum aligned sequence depth (genotype DP) required for each sample"
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
144 help="default: 0 (-d)" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
145 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
146
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
147 <xml name="min_gq">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
148 <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)">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
149 <validator type="in_range" min="0"/>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
150 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
151 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
152
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
153 <xml name="gt_pl_max">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
154 <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)" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
155 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
156 <token name="@VERSION@">0.18.1</token>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
157
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
158 <xml name="citations">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
159 <citations>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
160 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
161 <yield />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
162 </citations>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
163 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
164
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
165 <xml name="infile">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
166 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
167 <options options_filter_attribute="metadata.gemini_version" >
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
168 <filter type="add_value" value="@VERSION@" />
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
169 </options>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
170 <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>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
171 </param>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
172 </xml>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
173
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
174 </macros>