Mercurial > repos > gga > tripal_analysis_load_blast

comparison analysis_load_blast.xml @ 0:e1d4fad18572 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 05:50:16 -0400
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-1:000000000000 0:e1d4fad18572
1 <?xml version="1.0"?>
2 <tool id="analysis_load_blast" profile="16.04" name="Load Blast results" version="@WRAPPER_VERSION@.0">
3 <description>into Tripal</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <code file="tripal.py"/>
9 <expand macro="stdio"/>
10 <command><![CDATA[
11 tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
12
13 &&
14
15 cp '${blast_output}' "\${tmp_dir}/blast_input.xml"
16
17 &&
18
19 @AUTH@
20
21 tripaille analysis load_blast
22
23 --is_concat
24
25 --blastdb_id '${blastdb}'
26
27 --blast_parameters '${params}'
28
29 @MATCHING@
30
31 @ANALYSIS@
32
33 "\${tmp_dir}/blast_input.xml"
34
35 &&
36
37 echo "Data loaded" > $results
38 ]]></command>
39 <inputs>
40 <param name="blast_output"
41 type="data"
42 format="xml"
43 label="Blast blast_output" />
44
45 <param argument="--blastdb"
46 type="select"
47 dynamic_options="list_blastdbs()"
48 label="Blast databank used" />
49
50 <param name="params"
51 type="text"
52 label="Blast parameters used to produce the results" />
53
54 <expand macro="matching"/>
55
56 <expand macro="analysis" />
57 </inputs>
58 <outputs>
59 <data format="txt" name="results" label="Load Blast results into Tripal" />
60 </outputs>
61 <tests>
62 <test expect_failure="true" expect_exit_code="1">
63 <param name="blast_output" value="blast.xml" />
64 <param name="blastdb" value="genbank:protein" />
65 <param name="params" value="-e 0.001" />
66 <param name="query_type" value="mRNA" />
67 <param name="query_uniquename" value="true" />
68 <section name="analysis">
69 <param name="name" value="Some analysis" />
70 <param name="program" value="blastp" />
71 <param name="program_version" value="2.5.0" />
72 <param name="algorithm" value="blast" />
73 <param name="source" value="NCBI" />
74 <param name="source_version" value="1.0" />
75 <param name="source_uri" value="http://ncbi.com/somewhere" />
76 <param name="description" value="My cool new test analysis" />
77 <param name="date" value="2016-12-12" />
78 </section>
79
80 <expand macro="test_result" />
81 </test>
82 </tests>
83 <help><![CDATA[
84 @HELP_OVERVIEW@
85
86 **Load Blast results**
87
88 With this tool, you can load Blast results into the Tripal/Chado database.
89
90 A corresponding analysis will be created, keep in mind that you cannot add multiple analysis with the same program, program version and source.
91
92 The `tripal_analysis_blast <http://github.com/tripal/tripal_analysis_blast>`_ module must be installed and configured on the Tripal instance.
93
94 @HELP@
95 ]]></help>
96 <expand macro="citation"/>
97 </tool>