Mercurial > repos > gga > apollo_delete_features

annotate delete_features.xml @ 13:21a8cad7dfa5 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"
author gga
date Mon, 29 Jun 2020 09:12:19 -0400
parents df0e4eb2dfa5
children
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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="@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
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12 #if str($ask_one) == "yes":
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13 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
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14 python '$__tool_directory__/export.py'
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15 @ORG_OR_GUESS@
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16 --gff '$gff_out'
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17 --fasta_pep '$fasta_pep'
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18 --fasta_cds '$fasta_cds'
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19 --fasta_cdna '$fasta_cdna'
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20 --vcf '$vcf_out'
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21 --json '$json_out'
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22 '$__user_email__'
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24 &&
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25
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26 ## Now we delete
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27 python '$__tool_directory__/delete_features.py'
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28 @ORG_OR_GUESS@
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29 '$__user_email__'
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30 #if str($filter) != "all"
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31 --type $filter
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32 #end if
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33 > '$output';
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34 #else
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35 echo "Nothing to do" > '$output';
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <expand macro="org_or_guess" />
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40 <param name="filter" type="select" label="Feature Type Filter">
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41 <option value="all">All</option>
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42 <option value="mRNA">Genes</option>
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43 <option value="terminator">Terminators</option>
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44 <option value="tRNA">tRNAs</option>
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45 </param>
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46 <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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47 </inputs>
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48 <outputs>
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49 <data format="txt" name="output" label="Process and Error Log">
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50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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51 </data>
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52
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53 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
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54 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
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55 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
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56 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
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57 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
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58 <data format="json" name="json_out" label="Metadata from Apollo"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <conditional name="org_source">
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63 <param name="source_select" value="direct"/>
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64 <param name="org_raw" value="org4" />
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65 </conditional>
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66 <param name="filter" value="all"/>
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67 <param name="ask_one" value="yes"/>
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68
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69 <output name="gff_out">
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70 <assert_contents>
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71 <has_text text="##sequence-region Merlin 1 172788" />
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72 <has_text text="owner=admin@local.host;" />
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73 </assert_contents>
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74 </output>
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75 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
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76 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
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77 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
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78 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
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79 <output name="json_out">
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80 <assert_contents>
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81 <has_text text="org4" />
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82 <has_text text="apollo_shared_dir/org4" />
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83 </assert_contents>
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84 </output>
df0e4eb2dfa5 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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85 <output name="output">
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86 <assert_contents>
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87 <has_text text="Deleted" />
df0e4eb2dfa5 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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88 <has_text text="[type=mRNA]" />
df0e4eb2dfa5 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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89 </assert_contents>
df0e4eb2dfa5 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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90 </output>
0
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 **What it does**
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95
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96 Deletes every single one of the annotations on an organism. Intentionally.
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97
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98 **Why?**
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99
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100 There are legitimate uses for this tool, generally re-opened genomes is a good
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101 one. Needing to transfer annotations from one build of an organism to another
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102 (with the same refseq name).
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103
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104
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105 @REFERENCES@
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106 ]]></help>
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107 <expand macro="citations"/>
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108 </tool>