Mercurial > repos > gga > chado_feature_load_go

comparison feature_load_go.xml @ 0:cdf222d77b32 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
author gga
date Mon, 05 Nov 2018 08:06:39 -0500
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children 602218d4eef5
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-1:000000000000 0:cdf222d77b32
1 <?xml version="1.0"?>
2 <tool id="feature_load_go" name="Chado load GO annotation" 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 @AUTH@
11
12 chakin feature load_go
13 '$input'
14 '$organism_id'
15 '$analysis_id'
16
17 --query_type '$query_type'
18
19 $match_on_name
20
21 --name_column '$name_column'
22 --go_column '$go_column'
23
24 #if $re_name:
25 --re_name '$re_name'
26 #end if
27
28 $skip_missing
29
30 > $results
31 ]]></command>
32 <inputs>
33 <!-- arguments -->
34 <param name="input" label="GO annotation" argument="input" type="data" format="tabular" help="Path to the GO annotation file to load" />
35 <param argument="analysis_id" type="select" dynamic_options="list_analyses()" label="Analysis" />
36 <param argument="organism_id" type="select" dynamic_options="list_organisms()" label="Organism" />
37
38 <!-- options -->
39 <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" />
40
41 <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" />
42
43 <param name="name_column" label="Identifier column" argument="name_column" type="integer" value="2" help="Column containing the feature identifiers." />
44
45 <param name="go_column" label="GO column" argument="go_column" type="integer" value="5" help="Column containing the GO id." />
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 or GO id instead of aborting everything." />
52
53 <expand macro="wait_for"/>
54 </inputs>
55 <outputs>
56 <data format="txt" name="results"/>
57 </outputs>
58 <help>
59 Load GO annotation from a tabular file
60
61 @HELP@
62 </help>
63 </tool>