Mercurial > repos > gga > chado_organism_add_organism

comparison organism_add_organism.xml @ 10:7c212f0d1381 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 05:35:55 -0400
parents 7b552f5cb694
children e79da6f1f0da
comparison
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9:7b552f5cb694 10:7c212f0d1381
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@.0"> 2 <tool id="organism_add_organism" name="Chado organism add" version="@WRAPPER_VERSION@.1">
3 <description></description> 3 <description></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 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @AUTH@ 9 @START_PSQL@ &&
10 10
11 chakin organism add_organism 11 chakin organism add_organism
12 '$genus' 12 '$genus'
13 '$species' 13 '$species'
14 '$common' 14 '$common'
17 #if $comment: 17 #if $comment:
18 --comment '$comment' 18 --comment '$comment'
19 #end if 19 #end if
20 20
21 | jq -S . > '$results' 21 | jq -S . > '$results'
22
23 && @ZIP_PSQL@
22 ]]></command> 24 ]]></command>
23 <inputs> 25 <inputs>
24 <!-- arguments --> 26 <expand macro="psql_target"/>
27 <!-- arguments -->
25 <param name="genus" label="Genus" argument="genus" type="text" help="The genus of the organism" /> 28 <param name="genus" label="Genus" argument="genus" type="text" help="The genus of the organism" />
26 <param name="species" label="Species" argument="species" type="text" help="The species of the organism" /> 29 <param name="species" label="Species" argument="species" type="text" help="The species of the organism" />
27 <param name="common" label="Common" argument="common" type="text" help="The common name of the organism" /> 30 <param name="common" label="Common" argument="common" type="text" help="The common name of the organism" />
28 <param name="abbr" label="Abbr" argument="abbr" type="text" help="The abbreviation of the organism" /> 31 <param name="abbr" label="Abbr" argument="abbr" type="text" help="The abbreviation of the organism" />
29 32
30 <!-- options --> 33 <!-- options -->
31 <param name="comment" label="Comment" argument="--comment" type="text" help="A comment / description" /> 34 <param name="comment" label="Comment" argument="--comment" type="text" help="A comment / description" />
32 35
33 </inputs> 36 </inputs>
34 <outputs> 37 <outputs>
35 <data format="json" name="results"/> 38 <data format="json" name="results" label="Chado organism add: ${genus} ${species}"/>
39 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} '${genus} ${species}' on ${on_string}">
40 <filter>psql_target['method'] == "pgtools"</filter>
41 </data>
36 </outputs> 42 </outputs>
37 <help> 43 <help>
38 Add a new organism to the Chado database 44 Add a new organism to the Chado database
39 45
40 @HELP@ 46 @HELP@