Mercurial > repos > gga > tripal_analysis_load_interpro

comparison analysis_load_interpro.xml @ 0:a19926451daa draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:52:07 -0400
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1 <?xml version="1.0"?>
2 <tool id="analysis_load_interpro" profile="16.04" name="Load InterProScan results" version="@WRAPPER_VERSION@.0">
3 <description>into Tripal</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[
10 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
11
12 &&
13
14 cp '${input}' "\${tmp_dir}/interpro.xml"
15
16 &&
17
18 @AUTH@
19
20 tripaille analysis load_interpro
21
22 @ANALYSIS@
23
24 --interpro_parameters '${params}'
25
26 ${parse_go}
27
28 @MATCHING@
29
30 "\${tmp_dir}/interpro.xml"
31
32 &&
33
34 echo "Data loaded" > $results
35 ]]></command>
36 <inputs>
37 <param name="input"
38 type="data"
39 format="xml"
40 label="InterProScan results" />
41
42 <param name="parse_go"
43 type="boolean"
44 checked="true"
45 truevalue="--parse_go"
46 falsevalue=""
47 label="Load GO annotation to the database" />
48
49 <param name="params"
50 type="text"
51 label="InterProScan parameters used to produce the results" />
52
53 <expand macro="matching"/>
54 <expand macro="analysis" />
55 </inputs>
56 <outputs>
57 <data format="txt" name="results" label="Load InterProScan results into Tripal" />
58 </outputs>
59 <tests>
60 <test expect_failure="true" expect_exit_code="1">
61 <param name="input" value="interpro.xml" />
62 <param name="parse_go" value="true" />
63 <param name="params" value="--some --param" />
64 <param name="query_type" value="mRNA" />
65 <param name="query_uniquename" value="true" />
66 <section name="analysis">
67 <param name="name" value="Some analysis" />
68 <param name="program" value="interproscan" />
69 <param name="program_version" value="58.2" />
70 <param name="algorithm" value="interproscan" />
71 <param name="source" value="NCBI" />
72 <param name="source_version" value="1.0" />
73 <param name="source_uri" value="http://ncbi.com/somewhere" />
74 <param name="description" value="My cool new test analysis" />
75 <param name="date" value="2016-12-12" />
76 </section>
77
78 <expand macro="test_result" />
79 </test>
80 </tests>
81 <help><![CDATA[
82 @HELP_OVERVIEW@
83
84 **Load InterProScan results**
85
86 With this tool, you can load InterProScan results into the Tripal/Chado database.
87
88 A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.
89
90 The `tripal_analysis_interpro <http://github.com/tripal/tripal_analysis_interpro>`_ module must be installed and configured on the Tripal instance.
91
92 @HELP@
93 ]]></help>
94 <expand macro="citation"/>
95 </tool>