Mercurial > repos > eric-rasche > apollo
comparison delete_organism.xml @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
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children | f9a6e151b3b4 |
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1 <?xml version="1.0"?> | |
2 <tool id="edu.tamu.cpt2.webapollo.delete_organism" name="Delete an Apollo record" version="1.0"> | |
3 <description></description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <code file="webapollo.py"/> | |
8 <expand macro="requirements"/> | |
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 ## Now we delete | |
21 python $__tool_directory__/delete_organism.py | |
22 @ADMIN_AUTH@ | |
23 @ORG_OR_GUESS@ | |
24 "$__user_email__" | |
25 > $output; | |
26 #else | |
27 echo "Nothing to do" > $output; | |
28 #end if | |
29 #else | |
30 echo "Nothing to do" > $output; | |
31 #end if | |
32 ]]></command> | |
33 <inputs> | |
34 <expand macro="org_or_guess" /> | |
35 <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."/> | |
36 <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."/> | |
37 </inputs> | |
38 <outputs> | |
39 <data format="tabular" name="output" label="Process and Error Log"/> | |
40 | |
41 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> | |
42 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> | |
43 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> | |
44 </outputs> | |
45 <help><![CDATA[ | |
46 **What it does** | |
47 | |
48 Deletes every single one of the annotations on an organism. Intentionally. | |
49 | |
50 **Why?** | |
51 | |
52 There are legitimate uses for this tool, generally re-opened genomes is a good | |
53 one. Needing to transfer annotations from one build of an organism to another | |
54 (with the same refseq name). | |
55 | |
56 | |
57 @REFERENCES@ | |
58 ]]></help> | |
59 </tool> | |
60 |