Mercurial > repos > iuc > gemini_qc

annotate gemini_macros.xml @ 9:b46693c90f37 draft default tip

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 f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:02:36 +0000
parents 530211b4ec47
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
1 <macros>
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
2 <!-- gemini version to be used -->
4
22d275913efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 3
diff changeset
3 <token name="@VERSION@">0.20.1</token>
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
4 <!-- minimal annotation files version required by this version of gemini -->
4
22d275913efd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 3
diff changeset
5 <token name="@DB_VERSION@">200</token>
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
6
8
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
7 <xml name="bio_tools">
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
8 <xrefs>
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
9 <xref type="bio.tools">gemini</xref>
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
10 </xrefs>
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
11 </xml>
530211b4ec47 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
12
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
13 <xml name="requirements">
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
14 <requirements>
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
15 <requirement type="package" version="@VERSION@">gemini</requirement>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
16 <yield />
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
17 </requirements>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
18 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
19
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
20 <xml name="version_command">
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
21 <version_command>gemini --version</version_command>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
22 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
23
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
24 <xml name="stdio">
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
25 <stdio>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
26 <exit_code range="1:" />
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
27 <exit_code range=":-1" />
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
28 <regex match="Error:" />
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
29 <regex match="Exception:" />
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
30 <yield />
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
31 </stdio>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
32 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
33
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
34 <xml name="citations">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
35 <citations>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
36 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
37 <yield />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
38 </citations>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
39 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
40
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
41 <xml name="annotation_dir">
3
929c242be49a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 1
diff changeset
42 <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
43 <options from_data_table="gemini_versioned_databases">
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
44 <filter type="sort_by" column="0" />
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
45 <filter type="static_value" column="2" value="@DB_VERSION@" />
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
46 </options>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
47 </param>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
48 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
49
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
50 <xml name="infile">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
51 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
52 <options options_filter_attribute="metadata.gemini_version" >
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
53 <filter type="add_value" value="@VERSION@" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
54 </options>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
55 </param>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
56 </xml>
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
57
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
58 <xml name="add_header_column">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
59 <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
60 label="Add a header of column names to the output" />
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
61 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
62
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
63 <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
64 <conditional name="report">
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
65 <param name="report_selector" type="select"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
66 label="Set of columns to include in the variant report table"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
67 help="@HELP@">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
68 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
69 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
70 <option value="custom">Custom (report user-specified columns)</option>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
71 </param>
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
72 <when value="full" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
73 <when value="minimal">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
74 <param name="columns" type="hidden" value="@MINIMALSET@" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
75 <param name="extra_cols" type="hidden" value="" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
76 </when>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
77 <when value="custom">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
78 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
79 label="Choose columns to include in the report" help="(--columns)">
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
80 <option value="gene">gene</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
81 <option value="chrom">chrom</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
82 <option value="start">start</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
83 <option value="end">end</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
84 <option value="ref">ref</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
85 <option value="alt">alt</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
86 <option value="impact">impact</option>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
87 <option value="impact_severity">impact_severity</option>
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
88 <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
89 </param>
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
90 <param name="extra_cols" type="text"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
91 label="Additional columns (comma-separated)"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
92 help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output.">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
93 <expand macro="sanitize_query" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
94 </param>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
95 </when>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
96 </conditional>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
97 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
98
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
99 <xml name="filter" token_argument="--filter">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
100 <param argument="@ARGUMENT@" name="filter" type="text"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
101 label="Additional constraints expressed in SQL syntax"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
102 help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'.">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
103 <expand macro="sanitize_query" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
104 </param>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
105 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
106
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
107 <xml name="sanitize_query">
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
108 <sanitizer invalid_char="">
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
109 <valid initial="string.printable">
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
110 <remove value="&apos;" />
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
111 </valid>
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
112 <mapping initial="none">
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
113 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
114 </mapping>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
115 </sanitizer>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
116 </xml>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
117
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
118 <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below).">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
119 <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
120 label="Include hits with less convincing inheritance patterns"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
121 help= "@HELP@" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
122 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
123
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
124 <xml name="unaffected">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
125 <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
126 label="Report candidates shared by unaffected samples"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
127 help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
128 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
129
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
130 <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene.">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
131 <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
132 label="@LABEL@"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
133 help="@HELP@" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
134 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
135
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
136 <xml name="insert_constraint" token_max_repeat="1">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
137 <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
138 <expand macro="filter" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
139 <yield />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
140 </repeat>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
141 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
142
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
143 <xml name="overwritable_where_default" token_default_where="">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
144 <param name="overwrite_default_filter" type="boolean" checked="false"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
145 label="Overwrite the default constraint of this tool"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
146 help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
147 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
148
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
149 <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
150 <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
151 <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
152 label="Restrictions to apply to genotype values" help="">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
153 <expand macro="sanitize_query" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
154 <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
155 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
156 <yield />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
157 </repeat>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
158 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
159
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
160 <xml name="sample_filter">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
161 <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
162 <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
163 label="SQL filter to use to filter the sample table" help="">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
164 <expand macro="sanitize_query" />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
165 <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
166 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
167 <param argument="--in" name="in" type="select"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
168 label="A variant must be in either all, none or any samples passing the sample-query filter"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
169 help="">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
170 <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
171 <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
172 <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
173 <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
174 <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
175 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
176 <expand macro="min_kindreds"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
177 label="Minimum number of families in which a variant must pass the sample filter" help=""/>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
178 <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
179 label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." />
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
180 </repeat>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
181 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
182
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
183 <xml name="region_filter">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
184 <repeat name="regions" title="Region Filter" default="0" min="0"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
185 help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
186 <param name="chrom" type="text" label="Chromosome">
9
b46693c90f37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
iuc
parents: 8
diff changeset
187 <validator type="regex" message="A chromosome identifier is required when specifying a region filter. It should start with 'chr'">^chr[0-9a-zA-Z: _.-]+</validator>
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
188 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
189 <param name="start" type="text" label="Region Start">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
190 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
191 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
192 <param name="stop" type="text" label="Region End">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
193 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
194 </param>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
195 </repeat>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
196 </xml>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
197
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
198 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
199 mkdir gemini &&
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
200 ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
201 export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
202 ]]></token>
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
203
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
204 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
205 #set $sql_expr = str($multiline_sql_expr).strip()
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
206 #if str($sql_expr):
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
207 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
208 #set $sql_expr = $sql_expr.replace('\r', '\n')
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
209 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
210 $cmdln_param '$sql_expr'
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
211 #end if
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
212 </token>
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
213
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
214 <token name="@SET_COLS@">
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
215 #if str($report.report_selector) == 'full':
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
216 #set cols = "*"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
217 #else:
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
218 #if $report.columns and str($report.columns) != '':
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
219 #set $cols = str($report.columns)
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
220 #else
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
221 #set $cols = ''
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
222 #end if
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
223 #if str($report.extra_cols).strip():
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
224 #if $cols:
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
225 #set $cols = $cols + ', ' + str($report.extra_cols)
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
226 #else:
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
227 #set $cols = str($report.extra_cols)
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
228 #end if
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
229 #end if
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
230 #if not $cols:
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
231 #set $cols = "variant_id, gene"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
232 #end if
1
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
233 #end if
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
234 </token>
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
235
e923a49732d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 0
diff changeset
236 <token name="@COLUMN_SELECT@">
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
237 @SET_COLS@
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
238 #if $cols != "*"
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
239 --columns '$cols'
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
240 #end if
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
241 </token>
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
242
5
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
243 <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
244 #set $region_elements = []
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
245 #for $r in $regions:
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
246 ## The actual chromosome name needs to be single-quoted
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
247 ## in SQL, so we need to quote the single quotes like the
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
248 ## sanitize_query macro would if the whole was a parameter.
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
249 #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
250 #if str($r.start).strip():
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
251 #silent $r_elements.append("start >= %d" % int($r.start))
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
252 #end if
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
253 #if str($r.stop).strip():
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
254 #silent $r_elements.append("end <= %d" % int($r.stop))
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
255 #end if
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
256 #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
257 #end for
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
258 ]]>
8ee35a6b49de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
259 </token>
0
f44bb2b7bfc0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
260 </macros>