Mercurial > repos > gga > apollo_create_or_update
comparison create_or_update_organism.xml @ 0:cd595b5d890a draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:46:00 -0400 |
parents | |
children | b194ffbd6ae1 |
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-1:000000000000 | 0:cd595b5d890a |
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1 <?xml version="1.0"?> | |
2 <tool id="create_or_update" name="Create or Update Organism" version="3.2"> | |
3 <description>will create the organism if it doesn't exist, and update otherwise</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <code file="webapollo.py"/> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 cp -R '${jbrowse.extra_files_path}/data/' '@DATA_DIR@/${jbrowse.id}' | |
11 | |
12 && | |
13 | |
14 python $__tool_directory__/create_or_update_organism.py | |
15 | |
16 @ADMIN_AUTH@ | |
17 | |
18 --genus '$genus' | |
19 --species '$species' | |
20 #if str($group) != "None": | |
21 --group '${group}' | |
22 #end if | |
23 ${remove_old_directory} | |
24 $public | |
25 | |
26 @ORG_OR_GUESS@ | |
27 | |
28 '@DATA_DIR@/${jbrowse.id}' | |
29 | |
30 $__user_email__ | |
31 | |
32 > $output]]></command> | |
33 <inputs> | |
34 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> | |
35 <expand macro="org_or_guess" /> | |
36 <param name="genus" type="text" label="Genus" optional="False" /> | |
37 <param name="species" type="text" label="Species" optional="True" /> | |
38 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" /> | |
39 <param name="group" type="select" dynamic_options="galaxy_list_groups(__trans__)" label="Grant access to a user group" optional="True" /> | |
40 <param name="remove_old_directory" type="boolean" truevalue="--remove_old_directory" falsevalue="" label="Remove old data directory" /> | |
41 </inputs> | |
42 <outputs> | |
43 <data format="json" name="output"/> | |
44 </outputs> | |
45 <tests> | |
46 <test expect_failure="true"> | |
47 <param name="jbrowse" value="good-model.gff3"/> | |
48 <conditional name="org_source"> | |
49 <param name="source_select" value="direct"/> | |
50 <param name="org_raw" value="Test org" /> | |
51 </conditional> | |
52 <param name="genus" value="genus"/> | |
53 <assert_stderr> | |
54 <has_text text="cannot stat" /> | |
55 </assert_stderr> | |
56 </test> | |
57 </tests> | |
58 <help><![CDATA[ | |
59 **What it does** | |
60 | |
61 Adds an organism to the Apollo database. The tool takes the output of a | |
62 JBrowse run as that contains all of the necessary information for which | |
63 tracks are appropriate for a given analysis. | |
64 | |
65 **WARNINGS** | |
66 | |
67 - Do not use names which conflict with other users. | |
68 - If you provide an Apollo JSON file, only the first organism block will | |
69 be used in Common Name determination, as it is improbable you wish to | |
70 apply a single JBrowse instance to multiple organisms. | |
71 | |
72 @REFERENCES@ | |
73 ]]></help> | |
74 <expand macro="citations"/> | |
75 </tool> |