Mercurial > repos > iuc > vt_variant_tools
diff vt_normalize.xml @ 0:e4d445a95419 draft
Uploaded
author | iuc |
---|---|
date | Mon, 11 Aug 2014 14:10:22 -0400 |
parents | |
children | a5578ce1c0a1 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vt_normalize.xml Mon Aug 11 14:10:22 2014 -0400 @@ -0,0 +1,55 @@ +<tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0"> + <description>normalizes variants in a VCF file</description> + <expand macro="requirements" /> + <expand macro="version_command" /> + <macros> + <import>vt_macros.xml</import> + <token name="@BINARY@">normalize</token> + </macros> + <command> +<![CDATA[ + vt @BINARY@ + -o "${ outfile }" + ##-q do not print options and summary [] + -w window size for local sorting of variants [10000] + -I $intervals_file + ##-i intervals [] + -r $reference_genome + "${ infile }" +]]> + </command> + <expand macro="stdio" /> + <inputs> + <param name="infile" type="data" format="sqlite" label="GEMINI database" /> + + <param name="reference_genome" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="data_meta" ref="infile" key="dbkey" column="1" /> + <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> + </options> + </param> + + <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" /> + <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants" + help="(-w)"> + <validator type="in_range" min="0"/> + </param> + + </inputs> + <outputs> + <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> +**What it does** + +Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases, +the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs. + +@CITATION@ + </help> + <!--expand macro="citations"/--> +</tool>