Mercurial > repos > gga > apollo_delete_organism

annotate delete_organism.xml @ 11:b08ff873c9b2 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"
author gga
date Tue, 14 Apr 2020 10:42:05 -0400
parents dd63c6e11a95
children 6ea838bf1f2f
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1 <?xml version="1.0"?>
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2 <tool id="delete_organism" name="Delete an Apollo record" version="@WRAPPER_VERSION@" 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 @AUTH@
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11
0
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12 #if str($ask_one) == "yes":
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13 #if str($ask_two) == "yes":
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
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dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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15 python '$__tool_directory__/export.py'
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16 @ORG_OR_GUESS@
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17 --gff '$gff_out'
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18 --fasta_pep '$fasta_pep'
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19 --fasta_cds '$fasta_cds'
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20 --fasta_cdna '$fasta_cdna'
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21 --vcf '$vcf_out'
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22 --json '$json_out'
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23 '$__user_email__'
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24
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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25 &&
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26
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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27 ## Now we delete
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28 python '$__tool_directory__/delete_organism.py'
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29 @ORG_OR_GUESS@
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30 '$__user_email__'
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31 >> '$output';
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32 #else
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33 echo "Nothing to do" > '$output';
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34 #end if
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35 #else
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36 echo "Nothing to do" > '$output';
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <expand macro="org_or_guess" />
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41 <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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42 <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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43 </inputs>
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44 <outputs>
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45 <data format="json" name="output" label="Process and Error Log">
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46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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47 </data>
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48
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49 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
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50 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
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51 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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52 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
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53 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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54 <data format="json" name="json_out" label="Metadata from Apollo"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <conditional name="org_source">
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59 <param name="source_select" value="direct"/>
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60 <param name="org_raw" value="org3" />
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61 </conditional>
10
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62 <param name="ask_one" value="true"/>
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63 <param name="ask_two" value="true"/>
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64
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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65 <output name="gff_out">
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66 <assert_contents>
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67 <has_text text="##sequence-region Merlin 1 172788" />
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68 <has_text text="owner=admin@local.host;" />
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69 <has_text text="Name=cds-not-under-exon" />
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70 </assert_contents>
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71 </output>
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72 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
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73 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
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74 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
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75 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
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76 <output name="json_out">
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77 <assert_contents>
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78 <has_text text="org3" />
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79 <has_text text="Foo3" />
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80 </assert_contents>
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81 </output>
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82 <output name="output">
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83 <assert_contents>
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84 <has_text text="org3" />
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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85 <has_text text="Foo3" />
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86 </assert_contents>
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87 </output>
0
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88 </test>
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89 </tests>
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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90 <help><![CDATA[
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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91 **What it does**
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92
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93 Deletes every single one of the annotations on an organism. Intentionally.
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94
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95 **Why?**
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96
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97 There are legitimate uses for this tool, generally re-opened genomes is a good
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98 one. Needing to transfer annotations from one build of an organism to another
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99 (with the same refseq name).
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100
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101
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102 @REFERENCES@
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103 ]]></help>
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104 <expand macro="citations"/>
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105 </tool>