Mercurial > repos > eric-rasche > apollo
annotate delete_features.xml @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
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children | f9a6e151b3b4 |
rev | line source |
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5
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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1 <?xml version="1.0"?> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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2 <tool id="edu.tamu.cpt2.webapollo.delete_features" name="Delete all annotations from an Apollo record" version="1.2"> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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3 <description></description> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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4 <macros> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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5 <import>macros.xml</import> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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6 </macros> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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7 <code file="webapollo.py"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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8 <expand macro="requirements"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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9 <command detect_errors="aggressive"><![CDATA[ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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10 #if str($ask_one) == "yes": |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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11 #if str($ask_two) == "yes": |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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12 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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13 python $__tool_directory__/export.py |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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14 @ADMIN_AUTH@ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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15 @ORG_OR_GUESS@ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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16 --gff "$gff_out" |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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17 --fasta "$fasta_out" |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
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18 --json "$json_out"; |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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19 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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20 ## Now we delete |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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21 python $__tool_directory__/delete_features.py |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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22 @ADMIN_AUTH@ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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23 @ORG_OR_GUESS@ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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24 "$__user_email__" |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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25 > $output; |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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26 #else |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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27 echo "Nothing to do" > $output; |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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28 #end if |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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29 #else |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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30 echo "Nothing to do" > $output; |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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31 #end if |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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32 ]]></command> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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33 <inputs> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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changeset
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34 <expand macro="org_or_guess" /> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
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35 <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."/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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36 <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."/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
diff
changeset
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37 </inputs> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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38 <outputs> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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39 <data format="tabular" name="output" label="Process and Error Log"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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40 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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41 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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42 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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43 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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44 </outputs> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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45 <help><![CDATA[ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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46 **What it does** |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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47 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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48 Deletes every single one of the annotations on an organism. Intentionally. |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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49 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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50 **Why?** |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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51 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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52 There are legitimate uses for this tool, generally re-opened genomes is a good |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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53 one. Needing to transfer annotations from one build of an organism to another |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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54 (with the same refseq name). |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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55 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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56 |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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57 @REFERENCES@ |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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58 ]]></help> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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59 </tool> |
7610987e0c48
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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60 |