Mercurial > repos > gga > apollo_delete_features

annotate delete_features.xml @ 7:7d885dfe3966 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
author gga
date Fri, 15 Mar 2019 06:05:55 -0400
parents f7e9c792047b
children 2adc3aa47d15
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1 <?xml version="1.0"?>
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2 <tool id="delete_features" name="Delete all annotations from an Apollo record" version="1.6" 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 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
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12 python $__tool_directory__/export.py
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13 @ADMIN_AUTH@
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14 @ORG_OR_GUESS@
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15 --gff "$gff_out"
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16 --fasta "$fasta_out"
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17 --json "$json_out"
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18 "$__user_email__"
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19
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20 &&
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21
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22 ## Now we delete
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23 python $__tool_directory__/delete_features.py
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24 @ADMIN_AUTH@
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25 @ORG_OR_GUESS@
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26 "$__user_email__"
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27 #if str($filter) != "all"
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28 --type $filter
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29 #end if
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30 > $output;
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31 #else
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32 echo "Nothing to do" > $output;
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33 #end if
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34 ]]></command>
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35 <inputs>
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36 <expand macro="org_or_guess" />
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37 <param name="filter" type="select" label="Feature Type Filter">
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38 <option value="all">All</option>
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39 <option value="mRNA">Genes</option>
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40 <option value="terminator">Terminators</option>
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41 <option value="tRNA">tRNAs</option>
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42 </param>
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43 <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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44 </inputs>
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45 <outputs>
5
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46 <data format="tabular" name="output" label="Process and Error Log">
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47 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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48 </data>
0
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49
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50 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
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51 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
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52 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
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53 </outputs>
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54 <tests>
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55 <test expect_failure="true">
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56 <conditional name="org_source">
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57 <param name="source_select" value="direct"/>
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58 <param name="org_raw" value="Test org" />
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59 </conditional>
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60 <param name="filter" value="all"/>
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61 <param name="ask_one" value="yes"/>
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62 <expand macro="test_result" />
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 **What it does**
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67
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68 Deletes every single one of the annotations on an organism. Intentionally.
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69
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70 **Why?**
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71
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72 There are legitimate uses for this tool, generally re-opened genomes is a good
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73 one. Needing to transfer annotations from one build of an organism to another
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74 (with the same refseq name).
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75
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76
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77 @REFERENCES@
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78 ]]></help>
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79 <expand macro="citations"/>
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80 </tool>