Mercurial > repos > iuc > gemini_gene_wise
view gemini_gene_wise.xml @ 1:0db31ae5295e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 7867095d83e5d0e0f923de7e9720d59df0034817
author | iuc |
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date | Tue, 22 Mar 2016 21:42:10 -0400 |
parents | 99d6e7b1b7f1 |
children | bc66ebfd4159 |
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<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> <description>Custom genotype filtering by gene</description> <macros> <import>gemini_macros.xml</import> <token name="@BINARY@">gene_wise</token> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ gemini @BINARY@ #if int($min_filters) > 0: --min_filters $min_filters #end if #if $gt_filter.strip(): --gt-filter "${gt_filter}" #end if #if $report.report_selector != 'all': --columns "${report.columns}" #end if @CMDLN_SQL_FILTER_FILTER_OPTION@ "${ infile }" > "${ outfile }" ]]> </command> <inputs> <expand macro="infile" /> <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filter)"> <expand macro="sanitize_query" /> </param> <param name="min_filters" type="integer" value="0" min="0" label="Minimum number of filters" help="(--min-filters)" /> <expand macro="column_filter" /> <expand macro="filter" /> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <param name="infile" value="gemini_amend_input.db" ftype="gemini.sqlite" /> <param name="gt_filter" value="((gt_depths).(*).(>=1).(all))" /> <output name="outfile" file="gemini_gene_wise_result.tabular" /> </test> </tests> <help> <![CDATA[ **What it does** The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools. ]]> </help> <expand macro="citations"/> </tool>