Mercurial > repos > gga > tripal_expression_get_biomaterials

comparison expression_get_biomaterials.xml @ 0:de7d91ce970b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 869e5fd8535deca8325777efcd31c70a514b582a
author gga
date Mon, 25 Feb 2019 06:33:51 -0500
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1 <?xml version="1.0"?>
2 <tool id="expression_get_biomaterials" name="Get biomaterials" version="@WRAPPER_VERSION@.0">
3 <description>from Tripal</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package" version="1.5">jq</requirement>
9 </expand>
10 <code file="tripal.py"/>
11 <command detect_errors="aggressive"><![CDATA[
12 @AUTH@
13
14 tripaille expression get_biomaterials
15
16 #if $provider_id:
17 --provider_id '$provider_id'
18 #end if
19 #if $biomaterial_id:
20 --biomaterial_id '$biomaterial_id'
21 #end if
22 #if $organism_id:
23 --organism_id '$organism_id'
24 #end if
25 #if $dbxref_id:
26 --dbxref_id '$dbxref_id'
27 #end if
28
29 | jq -S . > $results
30 ]]></command>
31 <inputs>
32 <!-- arguments -->
33
34 <!-- options -->
35 <param argument="--organism_id" type="select" dynamic_options="list_organisms()" label="Organism" optional="true" />
36 <param name="provider_id" label="Provider Id" argument="provider_id" type="text" help="Limit query to the selected provider" />
37 <param name="biomaterial_id" label="Biomaterial Id" argument="biomaterial_id" type="text" help="Limit query to the selected biomaterial" />
38 <param name="dbxref_id" label="Dbxref Id" argument="dbxref_id" type="text" help="Limit query to the selected ref" />
39
40 </inputs>
41 <outputs>
42 <data format="json" name="results"/>
43 </outputs>
44 <help>
45 List biomaterials in the database
46
47 @HELP@
48 </help>
49 </tool>