Mercurial > repos > gga > chado_feature_get_features
annotate macros.xml @ 13:bce6bd348713 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
author | gga |
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date | Thu, 14 Nov 2019 10:00:36 -0500 |
parents | df8527b4f2b8 |
children | e1f3d846f41a |
rev | line source |
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0
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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1 <?xml version="1.0"?> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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2 <macros> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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3 <xml name="requirements"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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4 <requirements> |
12
df8527b4f2b8
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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5 <requirement type="package" version="@LIB_VERSION@">python-chado</requirement> |
1
91ba5a42d65e
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 53d8f1212a5602a4692517c44e0285228087e3f2
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6 <requirement type="package" version="1.5">jq</requirement> |
10
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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7 <requirement type="package" version="@PG_VERSION@">postgresql</requirement> |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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8 <requirement type="package" version="0.1">pglite</requirement> |
0
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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9 <yield/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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10 </requirements> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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11 </xml> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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12 |
13
bce6bd348713
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
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13 <token name="@LIB_VERSION@">2.3.1</token> |
12
df8527b4f2b8
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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14 <token name="@WRAPPER_VERSION@">@LIB_VERSION@</token> |
10
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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15 <token name="@PG_VERSION@">11.2</token> |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
gga
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16 |
0
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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17 <xml name="stdio"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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18 <stdio> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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19 <regex level="fatal" match="Exception:" source="stderr" /> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff
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20 <regex level="fatal" match="error" source="stderr" /> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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21 <exit_code range="1:" /> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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22 </stdio> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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23 </xml> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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24 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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25 <xml name="citation"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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26 <citations> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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27 </citations> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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28 </xml> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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29 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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30 <token name="@HELP_OVERVIEW@"><![CDATA[ |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
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31 **Python-chado Overview** |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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32 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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33 Python-cado provides several tools allowing to load data into a remote Chado database. |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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34 ]]></token> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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35 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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36 <token name="@HELP@"><![CDATA[ |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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37 ]]></token> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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38 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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39 <xml name="sanitized"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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40 <sanitizer> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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41 <valid initial="string.printable"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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42 <remove value="'"/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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43 </valid> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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44 <mapping initial="none"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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45 <add source="'" target="'"'"'"/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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46 <add source="(" target="\("/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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47 <add source=")" target="\)"/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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48 </mapping> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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49 </sanitizer> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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50 </xml> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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51 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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52 <!-- I'm not proud of it, but it is needed for workflows --> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
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53 <xml name="wait_for"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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54 <param name="wait_for" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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55 type="data" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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56 format="data" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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57 optional="true" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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58 label="Run this only after the following dataset is ready" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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59 help="Use this if you want to delay the job execution until some data is already loaded. The selected dataset will not be used for anything else."/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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parents:
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60 </xml> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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61 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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62 <xml name="feature_rel"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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63 <param name="rel_subject_re" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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64 argument="--rel-subject-re" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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65 type="text" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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66 label="Regular expression to extract the unique name of the parent feature" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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67 help="this regex will be applied on the fasta definition line to generate the unique name of the parent feature"> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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68 <expand macro="sanitized"/> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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69 </param> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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70 |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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71 <param name="rel_subject_type" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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72 argument="--rel-subject-type" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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73 type="text" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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74 label="Sequence type of the parent" |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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75 help="this should be a Sequence Ontology term" /> |
1494f2f25439
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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76 </xml> |
10
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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77 |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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78 <xml name="psql_target"> |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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79 <conditional name="psql_target"> |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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80 <param name="method" type="select" label="Chado Database" help="If you select 'Remote database' make sure credentials are defined in environment variables"> |
7028154f9c93
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 0b135f1ea2623ea68e41ac88e13d99e6b4ad8bea
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81 <option value="remote">Remote database</option> |
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82 <option value="pgtools">Database from history</option> |
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83 </param> |
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84 <when value="remote"/> |
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85 <when value="pgtools"> |
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86 <param name="infile" type="data" format="postgresql" label="Input database" /> |
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87 <param name="schema" type="text" label="Schema containing Chado tables" value="public" help="Can be 'chado' for a Tripal database"/> |
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88 </when> |
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89 </conditional> |
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90 </xml> |
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91 |
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92 <token name="@START_PSQL@"><![CDATA[ |
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93 #if $psql_target.method == 'pgtools' |
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94 tar -xjvf '$psql_target.infile' > /dev/null && |
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95 . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema' |
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96 #else |
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97 if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then |
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98 echo "__default: local" > '.auth.yml' && |
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99 echo "local:" >> '.auth.yml' && |
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100 echo " dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' && |
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101 echo " dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' && |
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102 echo " dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' && |
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103 echo " dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' && |
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104 echo " dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' && |
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105 echo " dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' && |
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106 |
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107 export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml' |
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108 ; fi |
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109 #end if |
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110 ]]></token> |
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111 |
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112 <token name="@STOP_PSQL@"><![CDATA[ |
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113 #if $psql_target.method == 'pgtools' |
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114 && |
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115 pglite stop -d ./postgresql && |
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116 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' |
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117 ; |
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118 ## Make sure psql is stopped even if loading script failed |
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119 pglite stop -d ./postgresql || true |
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120 #end if |
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121 ]]></token> |
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122 |
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123 <token name="@ZIP_PSQL@"><![CDATA[ |
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124 #if $psql_target.method == 'pgtools' |
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125 && |
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126 pglite stop -d ./postgresql && |
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127 timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' && |
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128 tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null |
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129 ; |
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130 ## Make sure psql is stopped even if loading script failed |
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131 pglite stop -d ./postgresql || true |
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132 #end if |
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133 ]]></token> |
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134 </macros> |