Mercurial > repos > eric-rasche > apollo
comparison create_or_update_organism.xml @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
parents | d4ae83dedb14 |
children | 8f76685cdfc8 |
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4:23ead6905145 | 5:7610987e0c48 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="edu.tamu.cpt2.webapollo.create_or_update" name="Create or Update Organism" version="3.0"> | 2 <tool id="edu.tamu.cpt2.webapollo.create_or_update" name="Create or Update Organism" version="3.1"> |
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 <code file="webapollo.py"/> | 7 <code file="webapollo.py"/> |
13 | 13 |
14 @ADMIN_AUTH@ | 14 @ADMIN_AUTH@ |
15 | 15 |
16 --genus "$genus" | 16 --genus "$genus" |
17 --species "$species" | 17 --species "$species" |
18 --group '${group}' | |
18 $public | 19 $public |
19 | 20 |
20 @ORG_OR_GUESS@ | 21 @ORG_OR_GUESS@ |
21 | 22 |
22 "@DATA_DIR@/${jbrowse.id}" | 23 "@DATA_DIR@/${jbrowse.id}" |
28 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> | 29 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> |
29 <expand macro="org_or_guess" /> | 30 <expand macro="org_or_guess" /> |
30 <param name="genus" type="text" label="Genus" optional="False" /> | 31 <param name="genus" type="text" label="Genus" optional="False" /> |
31 <param name="species" type="text" label="Species" optional="True" /> | 32 <param name="species" type="text" label="Species" optional="True" /> |
32 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" /> | 33 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" /> |
34 <param name="group" type="select" dynamic_options="galaxy_list_groups(__trans__)" label="Grant access to a user group" optional="True" /> | |
33 </inputs> | 35 </inputs> |
34 <outputs> | 36 <outputs> |
35 <data format="json" name="output"/> | 37 <data format="json" name="output"/> |
36 </outputs> | 38 </outputs> |
37 <help><![CDATA[ | 39 <help><![CDATA[ |