Mercurial > repos > gga > apollo_create_or_update

comparison create_or_update_organism.xml @ 10:d72192ec8e39 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:46:45 -0500
parents 29ce13734a5c
children 7609529caafa
comparison
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9:29ce13734a5c 10:d72192ec8e39
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="377">ucsc-fatotwobit</requirement> 8 <requirement type="package" version="377">ucsc-fatotwobit</requirement>
9 </expand> 9 </expand>
10 <code file="webapollo.py"/> 10 <code file="webapollo.py"/>
11 <command detect_errors="aggressive"><![CDATA[ 11 <command detect_errors="aggressive"><![CDATA[
12 @AUTH@
12 13
13 python $__tool_directory__/create_or_update_organism.py 14 python '$__tool_directory__/create_or_update_organism.py'
14
15 @ADMIN_AUTH@
16 15
17 --genus '$genus' 16 --genus '$genus'
18 --species '$species' 17 --species '$species'
19 #if str($group) != "None": 18 #if str($group) != "None":
20 --group '${group}' 19 --group '${group}'
21 #end if 20 #end if
22 21
22 --userid '$__user_id__'
23
23 ${remove_old_directory} 24 ${remove_old_directory}
25 ${no_reload_sequences}
24 $public 26 $public
25 27
26 @ORG_OR_GUESS@ 28 @ORG_OR_GUESS@
27 29
30 #if $test_hack == "yes":
31 ## When testing we can't access extra_files_path, but we know the path of test data
32 '$__tool_directory__/test-data/dataset_1_files/data/'
33 #else:
28 '${jbrowse.extra_files_path}/data/' 34 '${jbrowse.extra_files_path}/data/'
35 #end if
29 36
30 "@DATA_DIR@/${jbrowse.id}" 37 "@DATA_DIR@/${jbrowse.id}"
31 38
32 $__user_email__ 39 '$__user_email__'
33 40
34 > $output]]></command> 41 > '$output']]></command>
35 <inputs> 42 <inputs>
36 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> 43 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" />
37 <expand macro="org_or_guess" /> 44 <expand macro="org_or_guess" />
38 <param name="genus" type="text" label="Genus" optional="False" /> 45 <param name="genus" type="text" label="Genus" optional="False" />
39 <param name="species" type="text" label="Species" optional="True" /> 46 <param name="species" type="text" label="Species" optional="True" />
40 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" /> 47 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" />
41 <param name="group" type="select" dynamic_options="galaxy_list_groups(__trans__)" label="Grant access to a user group" optional="True" /> 48 <param name="group" type="select" dynamic_options="galaxy_list_groups(__trans__)" label="Grant access to a user group" optional="True" />
42 <param name="remove_old_directory" type="boolean" truevalue="--remove_old_directory" falsevalue="" label="Remove old data directory" /> 49 <param name="remove_old_directory" type="boolean" truevalue="--remove_old_directory" falsevalue="" label="Remove old data directory" />
50 <param name="no_reload_sequences" type="boolean" truevalue="" falsevalue="--no_reload_sequences" label="Update genome sequences" help="Select this if you want Apollo to reload the genome sequences when updating an existing organism. BEWARE! You will lose annotation data for all sequences that are not present anymore in the new jbrowse dataset." />
51 <param name="test_hack" type="hidden" value="no"/>
43 </inputs> 52 </inputs>
44 <outputs> 53 <outputs>
45 <data format="json" name="output"> 54 <data format="json" name="output">
46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 55 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
47 </data> 56 </data>
48 </outputs> 57 </outputs>
49 <tests> 58 <tests>
50 <test expect_failure="true"> 59 <test>
51 <param name="jbrowse" value="good-model.gff3"/> 60 <param name="jbrowse" value="dataset_1.dat"/>
52 <conditional name="org_source"> 61 <conditional name="org_source">
53 <param name="source_select" value="direct"/> 62 <param name="source_select" value="direct"/>
54 <param name="org_raw" value="Test org" /> 63 <param name="org_raw" value="Test org" />
55 </conditional> 64 </conditional>
56 <param name="genus" value="genus"/> 65 <param name="genus" value="genus"/>
57 <assert_stderr> 66 <param name="test_hack" value="yes"/>
58 <has_text text="cannot stat" /> 67 <output name="output" file="create_org/output.json" lines_diff="6"/>
59 </assert_stderr> 68 </test>
69 <test>
70 <!-- Send the same input to test updating -->
71 <param name="jbrowse" value="dataset_1.dat"/>
72 <conditional name="org_source">
73 <param name="source_select" value="direct"/>
74 <param name="org_raw" value="Test org" />
75 </conditional>
76 <param name="genus" value="genus2"/>
77 <param name="species" value="sp"/>
78 <param name="test_hack" value="yes"/>
79 <output name="output" file="create_org/output2.json" lines_diff="6"/>
60 </test> 80 </test>
61 </tests> 81 </tests>
62 <help><![CDATA[ 82 <help><![CDATA[
63 **What it does** 83 **What it does**
64 84