Mercurial > repos > gga > apollo_delete_features

annotate delete_features.xml @ 2:2a3057b52402 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 33ce5bd0cce35a12725b9ef9aed0683f3c41fbf9
author gga
date Wed, 20 Sep 2017 09:08:52 -0400
parents 4dd45d2fd904
children 40b26f8269a3
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4dd45d2fd904 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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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="1.5" 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
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19 &&
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20
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21 ## Now we delete
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22 python $__tool_directory__/delete_features.py
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23 @ADMIN_AUTH@
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24 @ORG_OR_GUESS@
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25 "$__user_email__"
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26 #if str($filter) != "all"
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27 --type $filter
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28 #end if
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29 > $output;
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30 #else
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31 echo "Nothing to do" > $output;
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <expand macro="org_or_guess" />
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36 <param name="filter" type="select" label="Feature Type Filter">
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37 <option value="all">All</option>
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38 <option value="mRNA">Genes</option>
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39 <option value="terminator">Terminators</option>
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40 <option value="tRNA">tRNAs</option>
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41 </param>
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42 <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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43 </inputs>
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44 <outputs>
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45 <data format="tabular" name="output" label="Process and Error Log"/>
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46
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47 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
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48 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
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49 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
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50 </outputs>
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51 <tests>
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52 <test expect_failure="true">
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53 <conditional name="org_source">
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54 <param name="source_select" value="direct"/>
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55 <param name="org_raw" value="Test org" />
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56 </conditional>
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57 <param name="filter" value="all"/>
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58 <param name="ask_one" 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>