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comparison create_features_from_gff3.xml @ 0:5aa3bc8d0253 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:45:37 -0400
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-1:000000000000 0:5aa3bc8d0253
1 <?xml version="1.0"?>
2 <tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="0.9">
3 <description></description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <code file="webapollo.py"/>
9 <command detect_errors="aggressive"><![CDATA[
10 python $__tool_directory__/create_features_from_gff3.py
11 @ADMIN_AUTH@
12 @ORG_OR_GUESS@
13
14 "$__user_email__"
15 '$gff3_data'
16 --source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}"
17
18 > $output]]></command>
19 <inputs>
20 <expand macro="org_or_guess" />
21 <expand macro="gff3_input" />
22 </inputs>
23 <outputs>
24 <data format="tabular" name="output" label="Process and Error Log"/>
25 </outputs>
26 <tests>
27 <test expect_failure="true">
28 <conditional name="org_source">
29 <param name="source_select" value="direct"/>
30 <param name="org_raw" value="Test org" />
31 </conditional>
32 <param name="gff3_data" value="good-model.gff3"/>
33 <expand macro="test_result" />
34 </test>
35 </tests>
36 <help><![CDATA[
37 **NOTA BENE**
38
39 This is **incredibly, highly experimental**
40
41 DO NOT:
42
43 - Run on gff3 referencing multiple reference sequences/contigs
44 - Expect it to work well
45 - Expect it to work at all
46
47 @REFERENCES@
48 ]]></help>
49 <expand macro="citations"/>
50 </tool>