Mercurial > repos > earlhaminst > ensembl_get_genetree

comparison get_genetree.xml @ 3:181e12d6ac96 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
author earlhaminst
date Fri, 24 Mar 2017 11:57:35 -0400
parents 950d9d11b6fb
children 0602dcf02768
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2:950d9d11b6fb 3:181e12d6ac96
22 </macros> 22 </macros>
23 <requirements> 23 <requirements>
24 <requirement type="package" version="2.12.4">requests</requirement> 24 <requirement type="package" version="2.12.4">requests</requirement>
25 <requirement type="package" version="1.10.0">six</requirement> 25 <requirement type="package" version="1.10.0">six</requirement>
26 </requirements> 26 </requirements>
27 <command> 27 <command detect_errors="exit_code">
28 <![CDATA[ 28 <![CDATA[
29 python $__tool_directory__/get_genetree.py 29 python '$__tool_directory__/get_genetree.py'
30 --id_type $input_type 30 --id_type $input_type
31 -i "$input" 31 -i '$input'
32 -g $species_selector 32 -g $species_selector
33 --format ${output_format.output_format_selector} 33 --format ${output_format.output_format_selector}
34 #if $output_format.output_format_selector == 'json' 34 #if $output_format.output_format_selector == 'json'
35 -s ${output_format.sequence.sequence_selector} 35 -s ${output_format.sequence.sequence_selector}
36 #if $output_format.sequence.sequence_selector != 'none' 36 #if $output_format.sequence.sequence_selector != 'none'
43 -a ${output_format.sequence.aligned} 43 -a ${output_format.sequence.aligned}
44 #end if 44 #end if
45 #else 45 #else
46 --nh_format $output_format.nh_format 46 --nh_format $output_format.nh_format
47 #end if 47 #end if
48 > "$output" 48 > '$output'
49 ]]> 49 ]]>
50 </command> 50 </command>
51 51
52 <inputs> 52 <inputs>
53 <param name="input_type" type="select" label="Input type"> 53 <param name="input_type" type="select" label="Input type">