Mercurial > repos > iuc > gemini
comparison gemini_region.xml @ 20:b5207530f991 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
| author | iuc |
|---|---|
| date | Tue, 29 Dec 2015 10:19:47 -0500 |
| parents | 27ce3de83007 |
| children |
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| 19:27ce3de83007 | 20:b5207530f991 |
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| 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> | |
| 2 <description>Extracting variants from specific regions or genes</description> | |
| 3 <macros> | |
| 4 <import>gemini_macros.xml</import> | |
| 5 <token name="@BINARY@">region</token> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
| 9 <expand macro="version_command" /> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 gemini @BINARY@ | |
| 13 | |
| 14 #if $region.region_selector == '--reg': | |
| 15 #if str(${region.region}) != '': | |
| 16 --reg "${region.region}" | |
| 17 #end if | |
| 18 #else: | |
| 19 #if str(${region.gene}) != '': | |
| 20 --gene "${region.gene}" | |
| 21 #end if | |
| 22 #end if | |
| 23 | |
| 24 #if $report.report_selector != 'all': | |
| 25 --columns "${report.columns}" | |
| 26 #end if | |
| 27 | |
| 28 @CMDLN_SQL_FILTER_FILTER_OPTION@ | |
| 29 | |
| 30 $header | |
| 31 "${ infile }" | |
| 32 > "${ outfile }" | |
| 33 ]]> | |
| 34 </command> | |
| 35 <inputs> | |
| 36 <expand macro="infile" /> | |
| 37 | |
| 38 <conditional name="region"> | |
| 39 <param name="region_selector" type="select" label="Select by ...?" help=""> | |
| 40 <option value="--reg">genomic coordinates</option> | |
| 41 <option value="--gene">gene name</option> | |
| 42 </param> | |
| 43 <when value="--reg"> | |
| 44 <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/> | |
| 45 </when> | |
| 46 <when value="--gene"> | |
| 47 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" /> | |
| 48 </when> | |
| 49 </conditional> | |
| 50 | |
| 51 <expand macro="column_filter" /> | |
| 52 <expand macro="filter" /> | |
| 53 | |
| 54 | |
| 55 <expand macro="add_header_column" /> | |
| 56 | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data name="outfile" format="tabular" /> | |
| 60 </outputs> | |
| 61 <tests> | |
| 62 <test> | |
| 63 </test> | |
| 64 </tests> | |
| 65 <help> | |
| 66 **What it does** | |
| 67 | |
| 68 One often is concerned with variants found solely in a particular gene or genomic region. | |
| 69 | |
| 70 @CITATION@ | |
| 71 </help> | |
| 72 <expand macro="citations"/> | |
| 73 </tool> |