Mercurial > repos > iuc > gemini_recessive_and_dominant
view gemini_autosomal_recessive.xml @ 2:4086bb81f52a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author | iuc |
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date | Thu, 09 Nov 2017 13:16:22 -0500 |
parents | 69ec574f6f41 |
children | 05124dc72dba |
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<tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.0"> <description>Find variants meeting an autosomal recessive/dominant model</description> <macros> <import>gemini_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ gemini #if str($rec_or_dom) == 'recessive': ## start autosomal_recessive autosomal_recessive #else: ## start autosomal_dominant autosomal_dominant #end if @COLUMN_SELECT@ @CMDLN_SQL_FILTER_FILTER_OPTION@ -d $d #if int($min_kindreds) > 0: --min-kindreds $min_kindreds #end if #if str($families).strip(): --families "$families" #end if $lenient $allow_unaffected #if int($min_gq) > 0: --min-gq $min_gq #end if #if int($gt_pl_max) > -1: --gt-pl-max $gt_pl_max #end if "${ infile }" > "${ outfile }" ]]> </command> <inputs> <param name="rec_or_dom" type="select" label="Autosomal ..." help=""> <option value="recessive">recessive</option> <option value="dominant">dominant</option> </param> <expand macro="infile" /> <expand macro="column_filter" /> <expand macro="filter" /> <expand macro="min_sequence_depth" /> <expand macro="family" /> <expand macro="lenient" /> <expand macro="unaffected" /> <expand macro="min_kindreds" /> <expand macro="min_gq" /> <expand macro="gt_pl_max" /> </inputs> <outputs> <data name="outfile" format="tabular" /> </outputs> <tests> <test> <param name="infile" value="gemini_autosomal_input.db" ftype="gemini.sqlite" /> <param name="rec_or_dom" value="dominant" /> <param name="report_selector" value="column_filter" /> <param name="columns" value="gene,chrom,impact" /> <param name="lenient" value="true" /> <output name="outfile" file="gemini_autosomal_dominant_result.tabular" /> </test> <test> <param name="infile" value="gemini_autosomal_input.db" ftype="gemini.sqlite" /> <param name="rec_or_dom" value="recessive" /> <param name="report_selector" value="column_filter" /> <param name="columns" value="gene,chrom,impact" /> <param name="lenient" value="true" /> <output name="outfile" file="gemini_autosomal_recessive.tabular" /> </test> </tests> <help> **What it does** Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern. The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts. </help> <expand macro="citations"/> </tool>