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annotate create_features_from_gff3.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"?>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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2 <tool id="edu.tamu.cpt2.webapollo.feat_from_gff3" name="GFF3 to Apollo Annotations" version="0.9">
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
eric-rasche
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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
eric-rasche
parents:
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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:
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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
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10 python $__tool_directory__/create_features_from_gff3.py
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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11 @ADMIN_AUTH@
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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12 @ORG_OR_GUESS@
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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14 "$__user_email__"
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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15 $gff3_data
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f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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16 --source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($input.history_id)}"
f9a6e151b3b4 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174
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17
5
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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18 > $output]]></command>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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19 <inputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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20 <expand macro="org_or_guess" />
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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21 <expand macro="gff3_input" />
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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22 </inputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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23 <outputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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24 <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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25 </outputs>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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26 <help><![CDATA[
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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27 **NOTA BENE**
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
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29 This is **incredibly, highly experimental**
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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31 DO NOT:
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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33 - Run on gff3 referencing multiple reference sequences/contigs
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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34 - Expect it to work well
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
eric-rasche
parents:
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35 - Expect it to work at all
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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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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37 @REFERENCES@
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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38 ]]></help>
7610987e0c48 planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
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39 </tool>