Mercurial > repos > gga > apollo_feat_from_gff3

comparison create_features_from_gff3.xml @ 10:5d1cf95ade8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:51:05 -0500
parents 09dacc7c6a21
children bb562d95b6cd
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9:09dacc7c6a21 10:5d1cf95ade8a
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="webapollo.py"/> 8 <code file="webapollo.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 python $__tool_directory__/create_features_from_gff3.py 10 @AUTH@
11 @ADMIN_AUTH@ 11
12 python '$__tool_directory__/create_features_from_gff3.py'
12 @ORG_OR_GUESS@ 13 @ORG_OR_GUESS@
13 14
14 "$__user_email__" 15 '$__user_email__'
15 '$gff3_data' 16 '$gff3_data'
16 --source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}" 17 --source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
17 18
18 > $output]]></command> 19 > '$output']]></command>
19 <inputs> 20 <inputs>
20 <expand macro="org_or_guess" /> 21 <expand macro="org_or_guess" />
21 <expand macro="gff3_input" /> 22 <expand macro="gff3_input" />
22 </inputs> 23 </inputs>
23 <outputs> 24 <outputs>
24 <data format="tabular" name="output" label="Process and Error Log"> 25 <data format="tabular" name="output" label="Process and Error Log">
25 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 26 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
26 </data> 27 </data>
27 </outputs> 28 </outputs>
28 <tests> 29 <tests>
29 <test expect_failure="true"> 30 <test>
30 <conditional name="org_source"> 31 <conditional name="org_source">
31 <param name="source_select" value="direct"/> 32 <param name="source_select" value="direct"/>
32 <param name="org_raw" value="Test org" /> 33 <param name="org_raw" value="Test org" />
33 </conditional> 34 </conditional>
34 <param name="gff3_data" value="good-model.gff3"/> 35 <param name="gff3_data" value="merlin.gff"/>
35 <expand macro="test_result" /> 36 <output name="output" file="load_gff3/output.tsv" compare="sim_size"/>
36 </test> 37 </test>
37 </tests> 38 </tests>
38 <help><![CDATA[ 39 <help><![CDATA[
39 **NOTA BENE** 40 **NOTA BENE**
40 41