Mercurial > repos > iuc > gemini_interactions

annotate gemini_macros.xml @ 6:47e49beb8e9b 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 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:24:55 -0500
parents e8983ed311bf
children 2b371de05377
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
1 <macros>
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
2 <!-- gemini version to be used -->
5
e8983ed311bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 4
diff changeset
3 <token name="@VERSION@">0.20.1</token>
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
4 <!-- minimal annotation files version required by this version of gemini -->
5
e8983ed311bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
iuc
parents: 4
diff changeset
5 <token name="@DB_VERSION@">200</token>
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
6
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
7 <xml name="requirements">
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
8 <requirements>
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
9 <requirement type="package" version="@VERSION@">gemini</requirement>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
10 <yield />
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
11 </requirements>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
12 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
13
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
14 <xml name="version_command">
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
15 <version_command>gemini --version</version_command>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
16 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
17
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
18 <xml name="stdio">
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
19 <stdio>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
20 <exit_code range="1:" />
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
21 <exit_code range=":-1" />
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
22 <regex match="Error:" />
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
23 <regex match="Exception:" />
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
24 <yield />
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
25 </stdio>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
26 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
27
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
28 <xml name="citations">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
29 <citations>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
30 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
31 <yield />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
32 </citations>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
33 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
34
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
35 <xml name="annotation_dir">
4
dd4dc1941e96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
36 <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
37 <options from_data_table="gemini_versioned_databases">
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
38 <filter type="sort_by" column="0" />
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
39 <filter type="static_value" column="2" value="@DB_VERSION@" />
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
40 </options>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
41 </param>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
42 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
43
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
44 <xml name="infile">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
45 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
46 <options options_filter_attribute="metadata.gemini_version" >
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
47 <filter type="add_value" value="@VERSION@" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
48 </options>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
49 </param>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
50 </xml>
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
51
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
52 <xml name="add_header_column">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
53 <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
54 label="Add a header of column names to the output" />
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
55 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
56
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
57 <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
58 <conditional name="report">
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
59 <param name="report_selector" type="select"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
60 label="Set of columns to include in the variant report table"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
61 help="@HELP@">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
62 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
63 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
64 <option value="custom">Custom (report user-specified columns)</option>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
65 </param>
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
66 <when value="full" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
67 <when value="minimal">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
68 <param name="columns" type="hidden" value="@MINIMALSET@" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
69 <param name="extra_cols" type="hidden" value="" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
70 </when>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
71 <when value="custom">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
72 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
73 label="Choose columns to include in the report" help="(--columns)">
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
74 <option value="gene">gene</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
75 <option value="chrom">chrom</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
76 <option value="start">start</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
77 <option value="end">end</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
78 <option value="ref">ref</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
79 <option value="alt">alt</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
80 <option value="impact">impact</option>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
81 <option value="impact_severity">impact_severity</option>
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
82 <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
83 </param>
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
84 <param name="extra_cols" type="text"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
85 label="Additional columns (comma-separated)"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
86 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.">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
87 <expand macro="sanitize_query" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
88 </param>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
89 </when>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
90 </conditional>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
91 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
92
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
93 <xml name="filter" token_argument="--filter">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
94 <param argument="@ARGUMENT@" name="filter" type="text"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
95 label="Additional constraints expressed in SQL syntax"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
96 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'.">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
97 <expand macro="sanitize_query" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
98 </param>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
99 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
100
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
101 <xml name="sanitize_query">
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
102 <sanitizer invalid_char="">
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
103 <valid initial="string.printable">
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
104 <remove value="&apos;" />
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
105 </valid>
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
106 <mapping initial="none">
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
107 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
108 </mapping>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
109 </sanitizer>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
110 </xml>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
111
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
112 <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).">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
113 <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
114 label="Include hits with less convincing inheritance patterns"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
115 help= "@HELP@" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
116 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
117
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
118 <xml name="unaffected">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
119 <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
120 label="Report candidates shared by unaffected samples"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
121 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."/>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
122 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
123
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
124 <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.">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
125 <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
126 label="@LABEL@"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
127 help="@HELP@" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
128 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
129
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
130 <xml name="insert_constraint" token_max_repeat="1">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
131 <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
132 <expand macro="filter" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
133 <yield />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
134 </repeat>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
135 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
136
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
137 <xml name="overwritable_where_default" token_default_where="">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
138 <param name="overwrite_default_filter" type="boolean" checked="false"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
139 label="Overwrite the default constraint of this tool"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
140 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." />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
141 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
142
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
143 <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
144 <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
145 <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
146 label="Restrictions to apply to genotype values" help="">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
147 <expand macro="sanitize_query" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
148 <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
149 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
150 <yield />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
151 </repeat>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
152 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
153
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
154 <xml name="sample_filter">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
155 <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
156 <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
157 label="SQL filter to use to filter the sample table" help="">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
158 <expand macro="sanitize_query" />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
159 <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
160 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
161 <param argument="--in" name="in" type="select"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
162 label="A variant must be in either all, none or any samples passing the sample-query filter"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
163 help="">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
164 <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
165 <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
166 <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
167 <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>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
168 <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>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
169 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
170 <expand macro="min_kindreds"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
171 label="Minimum number of families in which a variant must pass the sample filter" help=""/>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
172 <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
173 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." />
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
174 </repeat>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
175 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
176
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
177 <xml name="region_filter">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
178 <repeat name="regions" title="Region Filter" default="0" min="0"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
179 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.">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
180 <param name="chrom" type="text" label="Chromosome">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
181 <validator type="expression" message="A chromosome identifier is required when specifying a region filter">value.strip()</validator>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
182 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
183 <param name="start" type="text" label="Region Start">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
184 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
185 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
186 <param name="stop" type="text" label="Region End">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
187 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
188 </param>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
189 </repeat>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
190 </xml>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
191
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
192 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
193 mkdir gemini &&
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
194 ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
195 export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
196 ]]></token>
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
197
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
198 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
199 #set $sql_expr = str($multiline_sql_expr).strip()
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
200 #if str($sql_expr):
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
201 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
202 #set $sql_expr = $sql_expr.replace('\r', '\n')
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
203 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
204 $cmdln_param '$sql_expr'
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
205 #end if
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
206 </token>
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
207
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
208 <token name="@SET_COLS@">
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
209 #if str($report.report_selector) == 'full':
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
210 #set cols = "*"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
211 #else:
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
212 #if $report.columns and str($report.columns) != '':
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
213 #set $cols = str($report.columns)
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
214 #else
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
215 #set $cols = ''
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
216 #end if
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
217 #if str($report.extra_cols).strip():
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
218 #if $cols:
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
219 #set $cols = $cols + ', ' + str($report.extra_cols)
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
220 #else:
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
221 #set $cols = str($report.extra_cols)
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
222 #end if
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
223 #end if
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
224 #if not $cols:
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
225 #set $cols = "variant_id, gene"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
226 #end if
3
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
227 #end if
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
228 </token>
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
229
d3b3668b0ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
iuc
parents: 2
diff changeset
230 <token name="@COLUMN_SELECT@">
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
231 @SET_COLS@
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
232 #if $cols != "*"
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
233 --columns '$cols'
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
234 #end if
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
235 </token>
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
236
6
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
237 <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
238 #set $region_elements = []
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
239 #for $r in $regions:
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
240 ## The actual chromosome name needs to be single-quoted
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
241 ## in SQL, so we need to quote the single quotes like the
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
242 ## sanitize_query macro would if the whole was a parameter.
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
243 #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
244 #if str($r.start).strip():
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
245 #silent $r_elements.append("start >= %d" % int($r.start))
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
246 #end if
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
247 #if str($r.stop).strip():
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
248 #silent $r_elements.append("end <= %d" % int($r.stop))
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
249 #end if
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
250 #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
251 #end for
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
252 ]]>
47e49beb8e9b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 5
diff changeset
253 </token>
0
fe4c59c6bf3d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
parents:
diff changeset
254 </macros>