Mercurial > repos > gga > apollo_create_or_update

comparison create_or_update_organism.xml @ 7:cfeab429f660 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
author gga
date Fri, 15 Mar 2019 06:04:22 -0400
parents 696a1962212e
children 29ce13734a5c
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6:eb389ee1408e 7:cfeab429f660
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="create_or_update" name="Create or Update Organism" version="3.3"> 2 <tool id="create_or_update" name="Create or Update Organism" version="3.4">
3 <description>will create the organism if it doesn't exist, and update otherwise</description> 3 <description>will create the organism if it doesn't exist, and update otherwise</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements">
8 <requirement type="package" version="377">ucsc-fatotwobit</requirement>
9 </expand>
8 <code file="webapollo.py"/> 10 <code file="webapollo.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
10 cp -R '${jbrowse.extra_files_path}/data/' "@DATA_DIR@/${jbrowse.id}"
11
12 &&
13 12
14 python $__tool_directory__/create_or_update_organism.py 13 python $__tool_directory__/create_or_update_organism.py
15 14
16 @ADMIN_AUTH@ 15 @ADMIN_AUTH@
17 16
18 --genus '$genus' 17 --genus '$genus'
19 --species '$species' 18 --species '$species'
20 #if str($group) != "None": 19 #if str($group) != "None":
21 --group '${group}' 20 --group '${group}'
22 #end if 21 #end if
22
23 ${remove_old_directory} 23 ${remove_old_directory}
24 $public 24 $public
25 25
26 @ORG_OR_GUESS@ 26 @ORG_OR_GUESS@
27
28 '${jbrowse.extra_files_path}/data/'
27 29
28 "@DATA_DIR@/${jbrowse.id}" 30 "@DATA_DIR@/${jbrowse.id}"
29 31
30 $__user_email__ 32 $__user_email__
31 33