Mercurial > repos > iuc > gemini
comparison gemini_autosomal_recessive.xml @ 0:720cbfb4190d draft
Imported from capsule None
| author | iuc |
|---|---|
| date | Mon, 25 Aug 2014 17:15:54 -0400 |
| parents | |
| children | 93bb0cfacefb |
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| -1:000000000000 | 0:720cbfb4190d |
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| 1 <tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0"> | |
| 2 <description>Find variants meeting an autosomal recessive/dominant model</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>gemini_macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 gemini | |
| 11 | |
| 12 #if $rec_or_dom == 'recessive': | |
| 13 ## start autosomal_recessive | |
| 14 autosomal_recessive | |
| 15 #else: | |
| 16 ## start autosomal_dominant | |
| 17 autosomal_dominant | |
| 18 #end if | |
| 19 | |
| 20 #if $report.report_selector != 'all': | |
| 21 --columns "${report.columns}" | |
| 22 #end if | |
| 23 | |
| 24 #if $filter.filter_selector == 'yes': | |
| 25 --filter "${filter.filter}" | |
| 26 #end if | |
| 27 | |
| 28 -d $d | |
| 29 #if int($min_kindreds) > 0: | |
| 30 --min-kindreds $min_kindreds | |
| 31 #end if | |
| 32 | |
| 33 "${ infile }" | |
| 34 > "${ outfile }" | |
| 35 ]]> | |
| 36 </command> | |
| 37 <expand macro="stdio" /> | |
| 38 <inputs> | |
| 39 | |
| 40 <param name="rec_or_dom" type="select" label="Autosomal ..." help=""> | |
| 41 <option value="recessive">recessive</option> | |
| 42 <option value="dominant">dominant</option> | |
| 43 </param> | |
| 44 | |
| 45 <param name="infile" type="data" format="sqlite" label="GEMINI database" /> | |
| 46 <expand macro="column_filter" /> | |
| 47 <expand macro="filter" /> | |
| 48 <expand macro="min_sequence_depth" /> | |
| 49 <param name="min_kindreds" size="4" type="integer" value="-1" lebel="The min. number of kindreds that must have a candidate variant in a gene" | |
| 50 help="-1 means default values (--min-kindreds)" /> | |
| 51 | |
| 52 </inputs> | |
| 53 <outputs> | |
| 54 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 55 </outputs> | |
| 56 <tests> | |
| 57 <test> | |
| 58 </test> | |
| 59 </tests> | |
| 60 <help> | |
| 61 **What it does** | |
| 62 | |
| 63 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a | |
| 64 built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern. | |
| 65 The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts. | |
| 66 | |
| 67 @CITATION@ | |
| 68 </help> | |
| 69 <expand macro="citations"/> | |
| 70 </tool> |