Mercurial > repos > cropgeeks > flapjack

comparison favalleleheadercreator.xml @ 65:d7e91a614582 draft

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author cropgeeks
date Wed, 21 Feb 2018 11:54:51 -0500
parents 7448697d5b1d
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64:3b4e505bdad3 65:d7e91a614582
1 <tool id="intertek_to_flapjack_fav_allele" name="Intertek -> Flapjack favourable allele header formate" version="0.0.1"> 1 <tool id="intertek_flapjack_snp_sample_processor" name="Intertek / Flapjack - SNP Sample File Processor" version="0.0.1">
2 <description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description> 2 <description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description>
3 <command><![CDATA[ 3 <command><![CDATA[
4 java 4 java
5 #if $adv_opts.show_advanced 5 #if $adv_opts.show_advanced
6 -Xmx$adv_opts.memory 6 -Xmx$adv_opts.memory
7 #end if 7 #end if
8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.IntertekFavAlleleHeaderCreator 8 -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.IntertekFlapjackSnpSampleFileProcessor
9 -g $genotype 9 -g $genotype
10 -i $intertek 10 -i $intertek
11 -o $output 11 -o $output
12 ]]></command> 12 ]]></command>
13 <inputs> 13 <inputs>
14 <param format="txt" name="intertek" type="data" label="Intertek favourable allele file" 14 <param format="txt" name="intertek" type="data" label="Favourable allele file"
15 help="An Intertek file with favourable and unfavourable allele information for markers."/> 15 help="An Intertek file with favourable and unfavourable allele information for markers."/>
16 <param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file" 16 <param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file"
17 help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can 17 help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can
18 add the favourable and unfavourable allele information to this Flapjack genotype file." 18 add the favourable and unfavourable allele information to this Flapjack genotype file."
19 optional="true"/> 19 optional="true"/>