Mercurial > repos > gga > chado_expression_add_biomaterial

comparison expression_add_biomaterial.xml @ 5:9692e46b267a draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
author gga
date Mon, 08 Jul 2019 05:38:36 -0400
parents b0684eb7d975
children 8c7e2b5c228f
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4:b0684eb7d975 5:9692e46b267a
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="chado.py"/> 8 <code file="chado.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 @AUTH@ 10 @START_PSQL@ &&
11 11
12 chakin expression add_biomaterial 12 chakin expression add_biomaterial
13 13
14 #if $description: 14 #if $description:
15 --description '$description' 15 --description '$description'
32 32
33 '$biomaterial_name' 33 '$biomaterial_name'
34 '$organism_id' 34 '$organism_id'
35 35
36 | jq -S . > '$results' 36 | jq -S . > '$results'
37
38 && @ZIP_PSQL@
37 ]]></command> 39 ]]></command>
38 <inputs> 40 <inputs>
41 <expand macro="psql_target"/>
39 <!-- arguments --> 42 <!-- arguments -->
40 <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Biomaterial name" /> 43 <param name="biomaterial_name" label="Biomaterial Name" argument="biomaterial_name" type="text" help="Biomaterial name" />
41 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" /> 44 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
42 45
43 <!-- options --> 46 <!-- options -->
51 <expand macro="wait_for"/> 54 <expand macro="wait_for"/>
52 55
53 </inputs> 56 </inputs>
54 <outputs> 57 <outputs>
55 <data format="json" name="results"/> 58 <data format="json" name="results"/>
59 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${biomaterial_name}' on ${on_string}">
60 <filter>psql_target['method'] == "pgtools"</filter>
61 </data>
56 </outputs> 62 </outputs>
57 <help> 63 <help>
58 Add a new biomaterial to the database 64 Add a new biomaterial to the database
59 65
60 @HELP@ 66 @HELP@