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comparison delete_features.xml @ 0:4dd45d2fd904 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 05:46:21 -0400
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1 <?xml version="1.0"?>
2 <tool id="delete_features" name="Delete all annotations from an Apollo record" version="1.5" 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 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
12 python $__tool_directory__/export.py
13 @ADMIN_AUTH@
14 @ORG_OR_GUESS@
15 --gff "$gff_out"
16 --fasta "$fasta_out"
17 --json "$json_out"
18
19 &&
20
21 ## Now we delete
22 python $__tool_directory__/delete_features.py
23 @ADMIN_AUTH@
24 @ORG_OR_GUESS@
25 "$__user_email__"
26 #if str($filter) != "all"
27 --type $filter
28 #end if
29 > $output;
30 #else
31 echo "Nothing to do" > $output;
32 #end if
33 ]]></command>
34 <inputs>
35 <expand macro="org_or_guess" />
36 <param name="filter" type="select" label="Feature Type Filter">
37 <option value="all">All</option>
38 <option value="mRNA">Genes</option>
39 <option value="terminator">Terminators</option>
40 <option value="tRNA">tRNAs</option>
41 </param>
42 <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."/>
43 </inputs>
44 <outputs>
45 <data format="tabular" name="output" label="Process and Error Log"/>
46
47 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
48 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
49 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
50 </outputs>
51 <tests>
52 <test expect_failure="true">
53 <conditional name="org_source">
54 <param name="source_select" value="direct"/>
55 <param name="org_raw" value="Test org" />
56 </conditional>
57 <param name="filter" value="all"/>
58 <param name="ask_one" value="yes"/>
59 <expand macro="test_result" />
60 </test>
61 </tests>
62 <help><![CDATA[
63 **What it does**
64
65 Deletes every single one of the annotations on an organism. Intentionally.
66
67 **Why?**
68
69 There are legitimate uses for this tool, generally re-opened genomes is a good
70 one. Needing to transfer annotations from one build of an organism to another
71 (with the same refseq name).
72
73
74 @REFERENCES@
75 ]]></help>
76 <expand macro="citations"/>
77 </tool>