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comparison delete_organism.xml @ 0:dc738069b5ac 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 05:46:50 -0400
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1 <?xml version="1.0"?>
2 <tool id="delete_organism" name="Delete an Apollo record" version="1.0" profile="16.04">
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 #if str($ask_one) == "yes":
11 #if str($ask_two) == "yes":
12 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
13 python $__tool_directory__/export.py
14 @ADMIN_AUTH@
15 @ORG_OR_GUESS@
16 --gff "$gff_out"
17 --fasta "$fasta_out"
18 --json "$json_out"
19
20 &&
21
22 ## Now we delete
23 python $__tool_directory__/delete_organism.py
24 @ADMIN_AUTH@
25 @ORG_OR_GUESS@
26 "$__user_email__"
27 > $output;
28 #else
29 echo "Nothing to do" > $output;
30 #end if
31 #else
32 echo "Nothing to do" > $output;
33 #end if
34 ]]></command>
35 <inputs>
36 <expand macro="org_or_guess" />
37 <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
38 <param name="ask_two" type="boolean" truevalue="yes" falsevalue="" label="Are you really, really SURE you want to do this?" help="There's NO coming back from this."/>
39 </inputs>
40 <outputs>
41 <data format="tabular" name="output" label="Process and Error Log"/>
42
43 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
44 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
45 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
46 </outputs>
47 <tests>
48 <test expect_failure="true">
49 <conditional name="org_source">
50 <param name="source_select" value="direct"/>
51 <param name="org_raw" value="Test org" />
52 </conditional>
53 <param name="filter" value="all"/>
54 <param name="ask_one" value="yes"/>
55 <param name="ask_two" value="yes"/>
56 <expand macro="test_result" />
57 </test>
58 </tests>
59 <help><![CDATA[
60 **What it does**
61
62 Deletes every single one of the annotations on an organism. Intentionally.
63
64 **Why?**
65
66 There are legitimate uses for this tool, generally re-opened genomes is a good
67 one. Needing to transfer annotations from one build of an organism to another
68 (with the same refseq name).
69
70
71 @REFERENCES@
72 ]]></help>
73 <expand macro="citations"/>
74 </tool>