Mercurial > repos > gga > apollo_delete_organism

annotate delete_organism.xml @ 6:db98cd19587b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211
author gga
date Tue, 30 Oct 2018 04:32:00 -0400
parents 0af4179e6758
children 1575f11ac6fc
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1 <?xml version="1.0"?>
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2 <tool id="delete_organism" name="Delete an Apollo record" version="1.1" profile="16.04">
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3 <description></description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="webapollo.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 #if str($ask_one) == "yes":
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11 #if str($ask_two) == "yes":
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12 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
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13 python $__tool_directory__/export.py
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14 @ADMIN_AUTH@
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15 @ORG_OR_GUESS@
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16 --gff "$gff_out"
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17 --fasta "$fasta_out"
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18 --json "$json_out"
5
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19 "$__user_email__"
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20
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21 &&
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23 ## Now we delete
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24 python $__tool_directory__/delete_organism.py
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25 @ADMIN_AUTH@
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26 @ORG_OR_GUESS@
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27 "$__user_email__"
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28 > $output;
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29 #else
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30 echo "Nothing to do" > $output;
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31 #end if
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32 #else
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33 echo "Nothing to do" > $output;
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <expand macro="org_or_guess" />
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38 <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."/>
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39 <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."/>
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40 </inputs>
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41 <outputs>
5
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42 <data format="tabular" name="output" label="Process and Error Log">
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43 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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44 </data>
0
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45
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46 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
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47 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
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48 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
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49 </outputs>
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50 <tests>
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51 <test expect_failure="true">
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52 <conditional name="org_source">
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53 <param name="source_select" value="direct"/>
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54 <param name="org_raw" value="Test org" />
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55 </conditional>
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56 <param name="filter" value="all"/>
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57 <param name="ask_one" value="yes"/>
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58 <param name="ask_two" value="yes"/>
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59 <expand macro="test_result" />
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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64
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65 Deletes every single one of the annotations on an organism. Intentionally.
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66
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67 **Why?**
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68
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69 There are legitimate uses for this tool, generally re-opened genomes is a good
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70 one. Needing to transfer annotations from one build of an organism to another
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71 (with the same refseq name).
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72
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73
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74 @REFERENCES@
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75 ]]></help>
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76 <expand macro="citations"/>
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77 </tool>