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comparison splitbysample.xml @ 69:805b78c41bac draft

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author cropgeeks
date Wed, 21 Feb 2018 12:08:25 -0500
parents dc02f001fd09
children ca17d7295f9e
comparison
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68:dc02f001fd09 69:805b78c41bac
1 <tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1"> 1 <tool id="flapjack_split_by_sample" name="Flapjack Split By Sample" version="0.0.1">
2 <description>create a Flapjack project file from Flapjack formatted input files.</description> 2 <description>create a Flapjack project file from Flapjack formatted input files.</description>
3 <command><![CDATA[ 3 <command>
4 python $__tool_directory__/FlapjackProject.py 4 python $__tool_directory__/FlapjackProject.py
5 -j $__tool_directory__/lib/flapjack.jar 5 -j $__tool_directory__/lib/flapjack.jar
6 -g $genotypes 6 -g '$genotypes'
7 -s $traits 7 -s '$traits'
8 #if $map 8 #if $map
9 -m $map 9 -m '$map'
10 #end if
11 #if $name
12 -n $name
13 #end if 10 #end if
14 #if $qtls 11 #if $qtls
15 -q $qtls 12 -q '$qtls'
16 #end if 13 #end if
17 #if $adv_opts.show_advanced 14 #if $adv_opts.show_advanced
18 -M "$adv_opts.missingData" 15 -M "$adv_opts.missingData"
19 -S "$adv_opts.hetSep" 16 -S "$adv_opts.hetSep"
20 #end if 17 #end if
21 ]]>
22 </command> 18 </command>
23 <inputs> 19 <inputs>
24 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file" 20 <param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
25 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/> 21 help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
26 22