Mercurial > repos > gga > apollo_create_or_update
comparison create_or_update_organism.xml @ 7:cfeab429f660 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
author | gga |
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date | Fri, 15 Mar 2019 06:04:22 -0400 |
parents | 696a1962212e |
children | 29ce13734a5c |
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6:eb389ee1408e | 7:cfeab429f660 |
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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 |