Mercurial > repos > iuc > gemini
comparison gemini_query.xml @ 11:53a5647e5271 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 18 Feb 2015 11:36:37 -0500 |
| parents | 71dc82354595 |
| children | 65f742e605ec |
comparison
equal
deleted
inserted
replaced
| 10:0f1bcedd836f | 11:53a5647e5271 |
|---|---|
| 47 - -carrier-summary-by-phenotype CARRIER_SUMMARY | 47 - -carrier-summary-by-phenotype CARRIER_SUMMARY |
| 48 Output columns of counts of carriers and non-carriers | 48 Output columns of counts of carriers and non-carriers |
| 49 stratified by the given sample phenotype column--> | 49 stratified by the given sample phenotype column--> |
| 50 <expand macro="stdio" /> | 50 <expand macro="stdio" /> |
| 51 <inputs> | 51 <inputs> |
| 52 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | 52 <expand macro="infile" /> |
| 53 | 53 |
| 54 <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"> | 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" /> | 55 <expand macro="sanitize_query" /> |
| 56 </param> | 56 </param> |
| 57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"> | 57 <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"> |
| 71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/> | 71 label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/> |
| 72 | 72 |
| 73 <expand macro="add_header_column" /> | 73 <expand macro="add_header_column" /> |
| 74 | 74 |
| 75 <!-- TODO: is there any default values set? --> | 75 <!-- TODO: is there any default values set? --> |
| 76 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" /> | 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)" /> |
| 77 | 77 |
| 78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" | 78 <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" |
| 79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> | 79 label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/> |
| 80 | 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)"> | 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)"> |
| 88 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> | 88 <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/> |
| 89 | 89 |
| 90 | 90 |
| 91 </inputs> | 91 </inputs> |
| 92 <outputs> | 92 <outputs> |
| 93 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | 93 <data name="outfile" format="tabular" /> |
| 94 </outputs> | 94 </outputs> |
| 95 <tests> | 95 <tests> |
| 96 <test> | 96 <test> |
| 97 </test> | 97 </test> |
| 98 </tests> | 98 </tests> |