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comparison delete_features.xml @ 7:f9a6e151b3b4 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
author eric-rasche
date Tue, 27 Jun 2017 04:05:17 -0400
parents 7610987e0c48
children
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6:8f76685cdfc8 7:f9a6e151b3b4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt2.webapollo.delete_features" name="Delete all annotations from an Apollo record" version="1.2"> 2 <tool id="edu.tamu.cpt2.webapollo.delete_features" name="Delete all annotations from an Apollo record" version="1.5" profile="16.04">
3 <description></description> 3 <description></description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <code file="webapollo.py"/> 7 <code file="webapollo.py"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 #if str($ask_one) == "yes": 10 #if str($ask_one) == "yes":
11 #if str($ask_two) == "yes": 11 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
12 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. 12 python $__tool_directory__/export.py
13 python $__tool_directory__/export.py 13 @ADMIN_AUTH@
14 @ADMIN_AUTH@ 14 @ORG_OR_GUESS@
15 @ORG_OR_GUESS@ 15 --gff "$gff_out"
16 --gff "$gff_out" 16 --fasta "$fasta_out"
17 --fasta "$fasta_out" 17 --json "$json_out";
18 --json "$json_out";
19 18
20 ## Now we delete 19 ## Now we delete
21 python $__tool_directory__/delete_features.py 20 python $__tool_directory__/delete_features.py
22 @ADMIN_AUTH@ 21 @ADMIN_AUTH@
23 @ORG_OR_GUESS@ 22 @ORG_OR_GUESS@
24 "$__user_email__" 23 "$__user_email__"
25 > $output; 24 #if str($filter) != "all"
26 #else 25 --type $filter
27 echo "Nothing to do" > $output; 26 #end if
28 #end if 27 > $output;
29 #else 28 #else
30 echo "Nothing to do" > $output; 29 echo "Nothing to do" > $output;
31 #end if 30 #end if
32 ]]></command> 31 ]]></command>
33 <inputs> 32 <inputs>
34 <expand macro="org_or_guess" /> 33 <expand macro="org_or_guess" />
34 <param name="filter" type="select" label="Feature Type Filter">
35 <option value="all">All</option>
36 <option value="mRNA">Genes</option>
37 <option value="terminator">Terminators</option>
38 <option value="tRNA">tRNAs</option>
39 </param>
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."/> 40 <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> 41 </inputs>
38 <outputs> 42 <outputs>
39 <data format="tabular" name="output" label="Process and Error Log"/> 43 <data format="tabular" name="output" label="Process and Error Log"/>
40 44
41 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> 45 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
55 59
56 60
57 @REFERENCES@ 61 @REFERENCES@
58 ]]></help> 62 ]]></help>
59 </tool> 63 </tool>
60