Mercurial > repos > eric-rasche > apollo

annotate create_or_update_organism.xml @ 3:d4ae83dedb14 draft

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planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
author eric-rasche
date Thu, 12 Jan 2017 11:52:28 -0500
parents 6002cc0df04e
children 7610987e0c48
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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1 <?xml version="1.0"?>
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
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2 <tool id="edu.tamu.cpt2.webapollo.create_or_update" name="Create or Update Organism" version="3.0">
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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3 <description>will create the organism if it doesn't exist, and update otherwise</description>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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4 <macros>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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5 <import>macros.xml</import>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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6 </macros>
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
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7 <code file="webapollo.py"/>
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
parents:
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8 <expand macro="requirements"/>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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9 <command detect_errors="aggressive"><![CDATA[
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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10 cp -R ${jbrowse.extra_files_path}/data/ @DATA_DIR@/${jbrowse.id};
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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12 python $__tool_directory__/create_or_update_organism.py
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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14 @ADMIN_AUTH@
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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16 --genus "$genus"
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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17 --species "$species"
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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18 $public
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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20 @ORG_OR_GUESS@
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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22 "@DATA_DIR@/${jbrowse.id}"
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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24 $__user_email__
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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26 > $output]]></command>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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27 <inputs>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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28 <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" />
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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29 <expand macro="org_or_guess" />
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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30 <param name="genus" type="text" label="Genus" optional="False" />
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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31 <param name="species" type="text" label="Species" optional="True" />
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6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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32 <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" />
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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33 </inputs>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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34 <outputs>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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35 <data format="json" name="output"/>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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36 </outputs>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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37 <help><![CDATA[
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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38 **What it does**
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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39
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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40 Adds an organism to the Apollo database. The tool takes the output of a
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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41 JBrowse run as that contains all of the necessary information for which
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
eric-rasche
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42 tracks are appropriate for a given analysis.
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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43
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d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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44 **WARNINGS**
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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45
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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46 - Do not use names which conflict with other users.
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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47 - If you provide an Apollo JSON file, only the first organism block will
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
eric-rasche
parents: 0
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48 be used in Common Name determination, as it is improbable you wish to
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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49 apply a single JBrowse instance to multiple organisms.
d4ae83dedb14 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5
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50
0
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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51 @REFERENCES@
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52 ]]></help>
6002cc0df04e planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd
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53 </tool>