Mercurial > repos > iuc > gemini
diff 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 |
line wrap: on
line diff
--- a/gemini_region.xml Fri Oct 16 13:55:09 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> - <description>Extracting variants from specific regions or genes</description> - <macros> - <import>gemini_macros.xml</import> - <token name="@BINARY@">region</token> - </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> - <command> -<![CDATA[ - gemini @BINARY@ - - #if $region.region_selector == '--reg': - #if str(${region.region}) != '': - --reg "${region.region}" - #end if - #else: - #if str(${region.gene}) != '': - --gene "${region.gene}" - #end if - #end if - - #if $report.report_selector != 'all': - --columns "${report.columns}" - #end if - - @CMDLN_SQL_FILTER_FILTER_OPTION@ - - $header - "${ infile }" - > "${ outfile }" -]]> - </command> - <inputs> - <expand macro="infile" /> - - <conditional name="region"> - <param name="region_selector" type="select" label="Select by ...?" help=""> - <option value="--reg">genomic coordinates</option> - <option value="--gene">gene name</option> - </param> - <when value="--reg"> - <param name="region" type="text" label="Specify genomic region" help="e.g. chr1:100-200 (--reg)"/> - </when> - <when value="--gene"> - <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (--gene)" /> - </when> - </conditional> - - <expand macro="column_filter" /> - <expand macro="filter" /> - - - <expand macro="add_header_column" /> - - </inputs> - <outputs> - <data name="outfile" format="tabular" /> - </outputs> - <tests> - <test> - </test> - </tests> - <help> -**What it does** - -One often is concerned with variants found solely in a particular gene or genomic region. - -@CITATION@ - </help> - <expand macro="citations"/> -</tool>