Mercurial > repos > iuc > gemini
annotate gemini_query.xml @ 17:65f742e605ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:46:38 -0400 |
| parents | 53a5647e5271 |
| children | ce61d4876838 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> |
| 2 | 2 <description>Querying the GEMINI database</description> |
| 0 | 3 <macros> |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">query</token> | |
| 6 </macros> | |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
7 <expand macro="requirements" /> |
|
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
8 <expand macro="stdio" /> |
|
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
9 <expand macro="version_command" /> |
| 0 | 10 <command> |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 | |
| 2 | 14 --in "${in}" |
| 0 | 15 |
| 16 #if $gt_filter.strip(): | |
| 17 --gt-filter "${gt_filter}" | |
| 18 #end if | |
| 19 | |
| 20 #if $sample_filter.strip(): | |
| 21 --sample-filter "${sample_filter}" | |
| 22 #end if | |
| 23 | |
| 24 $show_samples | |
| 25 $show_families | |
| 26 $family_wise | |
| 27 $header | |
| 28 $dgidb | |
| 29 #if $region.strip(): | |
| 30 --region "${region}" | |
| 31 #end if | |
| 32 #if int($min_kindreds) > 0: | |
| 33 --min-kindreds $min_kindreds | |
| 34 #end if | |
| 35 ##--format FORMAT Format of output (JSON, TPED or default) # we will take default for the time being | |
| 36 ## --sample-delim STRING The delimiter to be used with the --show-samples option. | |
| 37 | |
| 2 | 38 #if $q.strip(): |
| 39 -q "${q}" | |
| 40 #end if | |
| 0 | 41 |
| 42 "${ infile }" | |
| 43 > "${ outfile }" | |
| 44 ]]> | |
| 45 </command> | |
| 46 <!-- | |
| 47 ##TODO: | |
| 48 - -carrier-summary-by-phenotype CARRIER_SUMMARY | |
| 49 Output columns of counts of carriers and non-carriers | |
| 50 stratified by the given sample phenotype column--> | |
| 51 <inputs> | |
| 11 | 52 <expand macro="infile" /> |
| 0 | 53 |
| 8 | 54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"> |
| 55 <expand macro="sanitize_query" /> | |
| 56 </param> | |
| 57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"> | |
| 58 <expand macro="sanitize_query" /> | |
| 59 </param> | |
| 60 <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"> | |
| 61 <expand macro="sanitize_query" /> | |
| 62 </param> | |
| 0 | 63 |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
64 <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" |
| 0 | 65 label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/> |
| 66 | |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
67 <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" |
| 0 | 68 label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/> |
| 69 | |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
70 <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" |
| 0 | 71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/> |
| 72 | |
| 73 <expand macro="add_header_column" /> | |
| 74 | |
| 75 <!-- TODO: is there any default values set? --> | |
| 11 | 76 <param name="min_kindreds" size="4" type="integer" value="-1" label="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" /> |
| 0 | 77 |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" |
| 0 | 79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> |
| 80 | |
| 81 <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)"> | |
| 2 | 82 <option value="all">Return a variant if all samples matching the query have the variant. (all)</option> |
| 83 <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option> | |
| 84 <option value="any">Return all of the variant which are in all of the matching samples and not in any of the non-matching samples. (any)</option> | |
| 85 <option value="only">Return a variant if the variant is only in the matching samples and not in any of the non-matching samples. (only)</option> | |
| 0 | 86 </param> |
| 87 | |
| 88 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> | |
| 89 | |
| 90 | |
| 91 </inputs> | |
| 92 <outputs> | |
| 11 | 93 <data name="outfile" format="tabular" /> |
| 0 | 94 </outputs> |
| 95 <tests> | |
| 96 <test> | |
| 97 </test> | |
| 98 </tests> | |
| 99 <help> | |
| 100 **What it does** | |
| 101 | |
|
17
65f742e605ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
11
diff
changeset
|
102 The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. |
| 0 | 103 The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants! |
| 104 | |
| 105 http://gemini.readthedocs.org/en/latest/content/querying.html | |
| 106 | |
| 107 @CITATION@ | |
| 108 </help> | |
| 109 <expand macro="citations"/> | |
| 110 </tool> |