Mercurial > repos > gga > chado_load_blast

comparison load_blast.xml @ 0:1daff3b60f39 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
author gga
date Wed, 21 Aug 2019 05:13:05 -0400
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children f23cfcb0ab8c
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-1:000000000000 0:1daff3b60f39
1 <?xml version="1.0"?>
2 <tool id="load_blast" name="Chado load Blast results" version="@WRAPPER_VERSION@.0">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <code file="chado.py"/>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[
10 @START_PSQL@ &&
11
12 chakin load blast
13 '$analysis_id'
14 '$organism_id'
15 '$input'
16
17 --blastdb_id '$blastdb_id'
18
19 --query_type '$query_type'
20
21 $match_on_name
22
23 #if $re_name:
24 --re_name '$re_name'
25 #end if
26
27 $skip_missing
28
29 | jq -S . > $results
30
31 @ZIP_PSQL@
32 ]]></command>
33 <inputs>
34 <expand macro="psql_target"/>
35 <!-- arguments -->
36 <param name="input" label="Blast results" argument="input" type="data" format="xml" help="Path to the Blast XML file to load" />
37 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
38 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
39
40 <!-- options -->
41 <param name="query_type" label="Query type" argument="--query_type" type="text" help="The feature type (e.g. 'gene', 'mRNA', 'polypeptide', 'contig') of the query. It must be a valid Sequence Ontology term." value="polypeptide" />
42
43 <param name="match_on_name" label="Match On Name" argument="--match_on_name" type="boolean" truevalue="--match_on_name" falsevalue="" help="Match features using their name instead of their uniquename" />
44
45 <param argument="blastdb_id" type="select" dynamic_options="list_dbs()" label="Database blasted against" />
46
47 <param name="re_name" label="Name regular expression" argument="--re_name" type="text" help="Regular expression to extract the feature name from the input file (first capturing group will be used)." optional="true">
48 <expand macro="sanitized"/>
49 </param>
50
51 <param name="skip_missing" label="Skip Missing" argument="--skip_missing" type="boolean" truevalue="--skip_missing" falsevalue="" help="Skip lines with unknown features instead of aborting everything." />
52
53 <expand macro="wait_for"/>
54 </inputs>
55 <outputs>
56 <data format="json" name="results"/>
57 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
58 <filter>psql_target['method'] == "pgtools"</filter>
59 </data>
60 </outputs>
61 <help>
62 Load a blast analysis, in the same way as does the tripal_analysis_blast module
63
64 @HELP@
65 </help>
66 </tool>