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annotate delete_features.xml @ 8:df7a90763b3c draft default tip

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 37aa8fa02c144220da9a3899644025b8c19697c9
author eric-rasche
date Tue, 27 Jun 2017 04:13:27 -0400
parents f9a6e151b3b4
children
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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1 <?xml version="1.0"?>
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
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2 <tool id="edu.tamu.cpt2.webapollo.delete_features" name="Delete all annotations from an Apollo record" version="1.5" profile="16.04">
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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3 <description></description>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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4 <macros>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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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
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6 </macros>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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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
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8 <expand macro="requirements"/>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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9 <command detect_errors="aggressive"><![CDATA[
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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10 #if str($ask_one) == "yes":
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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11 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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12 python $__tool_directory__/export.py
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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13 @ADMIN_AUTH@
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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14 @ORG_OR_GUESS@
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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15 --gff "$gff_out"
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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16 --fasta "$fasta_out"
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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17 --json "$json_out";
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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18
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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19 ## Now we delete
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
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20 python $__tool_directory__/delete_features.py
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 5
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21 @ADMIN_AUTH@
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
eric-rasche
parents: 5
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22 @ORG_OR_GUESS@
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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23 "$__user_email__"
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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24 #if str($filter) != "all"
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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25 --type $filter
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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26 #end if
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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27 > $output;
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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28 #else
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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29 echo "Nothing to do" > $output;
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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30 #end if
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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31 ]]></command>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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32 <inputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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33 <expand macro="org_or_guess" />
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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34 <param name="filter" type="select" label="Feature Type Filter">
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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35 <option value="all">All</option>
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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36 <option value="mRNA">Genes</option>
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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37 <option value="terminator">Terminators</option>
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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38 <option value="tRNA">tRNAs</option>
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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parents: 5
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39 </param>
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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40 <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
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41 </inputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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42 <outputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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43 <data format="tabular" name="output" label="Process and Error Log"/>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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44
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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45 <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
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46 <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
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47 <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
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48 </outputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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49 <help><![CDATA[
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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50 **What it does**
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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51
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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52 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
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53
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54 **Why?**
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56 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
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57 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
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58 (with the same refseq name).
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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61 @REFERENCES@
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62 ]]></help>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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63 </tool>